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This page was generated on 2022-01-19 11:11:50 -0500 (Wed, 19 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 merida1


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: 2022-01-18 13:55:18 -0500 (Tue, 18 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.47.0.tar.gz
StartedAt: 2022-01-19 02:19:07 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 02:30:35 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 688.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:lumi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings lumi_2.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 81.556  8.459  90.122
methylationCall  5.592  0.440   6.039
getChipInfo      5.685  0.249   5.989
plotGammaFit     5.105  0.520   5.632
MAplot-methods   5.126  0.067   5.204
gammaFitEM       4.634  0.503   5.142
nuID2IlluminaID  5.094  0.039   5.140
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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-class1.9840.1312.117
MAplot-methods5.1260.0675.204
addAnnotationInfo0.0920.0040.095
addControlData2lumi0.0000.0010.000
addNuID2lumi000
adjColorBias.quantile2.1350.0782.217
adjColorBias.ssn0.6080.0250.635
bgAdjust0.1120.0020.115
bgAdjustMethylation0.2670.0200.287
boxplot-MethyLumiM-methods0.7810.0140.796
boxplot-methods0.1280.0030.132
boxplotColorBias1.2140.0151.231
density-methods0.1260.0030.130
detectOutlier0.1270.0050.131
detectionCall0.2210.0060.228
estimateBeta0.2860.0080.295
estimateIntensity0.3220.0080.332
estimateLumiCV0.1330.0030.138
estimateM0.7230.0190.744
estimateMethylationBG0.2050.0050.211
example.lumi0.1060.0030.109
example.lumiMethy0.0880.0020.090
example.methyTitration0.2560.0060.262
gammaFitEM4.6340.5035.142
getChipInfo5.6850.2495.989
getControlData0.0020.0000.002
getControlProbe0.0010.0000.002
getControlType0.0010.0010.001
getNuIDMappingInfo1.6030.0741.683
hist-methods0.1730.0030.177
id2seq0.0010.0000.001
inverseVST0.7560.0220.780
is.nuID0.0000.0000.001
lumiB0.1360.0030.139
lumiExpresso0.3310.0110.344
lumiMethyB0.0990.0030.102
lumiMethyC1.5140.0761.596
lumiMethyN0.1330.0030.137
lumiMethyStatus81.556 8.45990.122
lumiN0.6460.0320.679
lumiQ0.3960.0130.410
lumiR000
lumiR.batch000
lumiT0.4530.0190.476
methylationCall5.5920.4406.039
normalizeMethylation.quantile0.2420.0220.264
normalizeMethylation.ssn0.2270.0040.233
nuID2EntrezID1.5450.0261.574
nuID2IlluminaID5.0940.0395.140
nuID2RefSeqID1.4650.0211.487
nuID2probeID4.7220.0254.757
nuID2targetID4.7390.0354.785
pairs-methods1.3050.0471.359
plot-methods2.3970.0492.459
plotCDF0.1830.0060.191
plotColorBias1D0.2680.0070.277
plotColorBias2D0.2590.0060.267
plotControlData0.0010.0010.002
plotDensity0.1550.0030.158
plotGammaFit5.1050.5205.632
plotHousekeepingGene0.0010.0000.001
plotSampleRelation1.1430.0291.177
plotStringencyGene0.0010.0010.002
plotVST0.4500.0130.471
probeID2nuID4.9230.0234.961
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id0.0000.0010.001
targetID2nuID4.8940.0244.928
vst0.2760.0060.283