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This page was generated on 2022-01-18 11:05:55 -0500 (Tue, 18 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
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? 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 1017/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.47.0  (landing page)
Lei Huang
Snapshot Date: 2022-01-17 13:55:17 -0500 (Mon, 17 Jan 2022)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: master
git_last_commit: 2336503
git_last_commit_date: 2021-10-26 11:50:43 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'Biobase' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: lumi
Version: 2.47.0
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_2.47.0.tar.gz
StartedAt: 2022-01-17 19:43:10 -0500 (Mon, 17 Jan 2022)
EndedAt: 2022-01-17 19:49:26 -0500 (Mon, 17 Jan 2022)
EllapsedTime: 376.1 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_2.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘2.47.0’
* 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 39.790  0.104  39.896
MAplot-methods   5.438  0.024   5.461
* 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-class0.9490.0601.009
MAplot-methods5.4380.0245.461
addAnnotationInfo0.0470.0120.059
addControlData2lumi000
addNuID2lumi0.0000.0010.000
adjColorBias.quantile0.6570.0110.669
adjColorBias.ssn0.3570.0000.357
bgAdjust0.0690.0040.073
bgAdjustMethylation0.1320.0000.132
boxplot-MethyLumiM-methods0.4240.0080.433
boxplot-methods0.0750.0040.080
boxplotColorBias1.0570.0041.061
density-methods0.0770.0040.080
detectOutlier0.0730.0040.077
detectionCall0.1260.0040.130
estimateBeta0.1240.0040.128
estimateIntensity0.1500.0070.158
estimateLumiCV0.0860.0000.086
estimateM0.4350.0400.478
estimateMethylationBG0.1030.0000.102
example.lumi0.0650.0040.069
example.lumiMethy0.0490.0000.048
example.methyTitration0.1610.0000.162
gammaFitEM2.0860.0042.091
getChipInfo4.3230.2684.702
getControlData0.0010.0000.002
getControlProbe0.0010.0000.001
getControlType0.0010.0000.001
getNuIDMappingInfo0.8370.0400.890
hist-methods0.1930.0000.193
id2seq0.0000.0010.001
inverseVST0.3840.0300.414
is.nuID0.0010.0000.001
lumiB0.0850.0080.093
lumiExpresso0.4170.0040.421
lumiMethyB0.0530.0000.053
lumiMethyC0.7530.0000.753
lumiMethyN0.0810.0040.085
lumiMethyStatus39.790 0.10439.896
lumiN0.4140.0040.418
lumiQ0.2570.0000.257
lumiR000
lumiR.batch000
lumiT0.2940.0040.297
methylationCall1.9980.0122.011
normalizeMethylation.quantile0.1550.0040.159
normalizeMethylation.ssn0.1120.0000.113
nuID2EntrezID0.7140.0080.723
nuID2IlluminaID3.3560.0023.357
nuID2RefSeqID1.0080.0121.021
nuID2probeID2.9440.0002.944
nuID2targetID2.9770.0212.999
pairs-methods0.6800.0080.689
plot-methods1.7800.0121.792
plotCDF0.140.000.14
plotColorBias1D0.180.000.18
plotColorBias2D0.1480.0000.148
plotControlData0.0000.0010.001
plotDensity0.0970.0100.108
plotGammaFit3.9380.0003.938
plotHousekeepingGene0.0010.0000.001
plotSampleRelation0.3840.0000.384
plotStringencyGene0.0010.0000.001
plotVST0.3110.0000.311
probeID2nuID3.0950.0003.095
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile0.0000.0000.001
seq2id0.0000.0000.001
targetID2nuID3.0140.0003.015
vst0.160.000.16