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This page was generated on 2023-02-02 11:10:19 -0500 (Thu, 02 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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? 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 1052/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.51.0  (landing page)
Lei Huang
Snapshot Date: 2023-02-01 14:00:21 -0500 (Wed, 01 Feb 2023)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: master
git_last_commit: 95a906f
git_last_commit_date: 2022-11-01 10:42:41 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 2.51.0
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_2.51.0.tar.gz
StartedAt: 2023-02-02 02:58:56 -0500 (Thu, 02 Feb 2023)
EndedAt: 2023-02-02 03:16:02 -0500 (Thu, 02 Feb 2023)
EllapsedTime: 1026.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### 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_2.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lumi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lumi’ version ‘2.51.0’
* 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 ... NOTE
checkRd: (-1) addNuID2lumi.Rd:21: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) getChipInfo.Rd:22: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) getNuIDMappingInfo.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) lumiR.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) lumiR.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) lumiR.Rd:36: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_
checkRd: (-1) lumiR.Rd:40: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) lumiR.batch.Rd:24: Escaped LaTeX specials: \_ \_ \_ \_ \_
checkRd: (-1) nuID2EntrezID.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) nuID2IlluminaID.Rd:21: Escaped LaTeX specials: \_ \_
checkRd: (-1) nuID2RefSeqID.Rd:19: Escaped LaTeX specials: \_
checkRd: (-1) produceGEOSampleInfoTemplate.Rd:18: Escaped LaTeX specials: \_ \_
checkRd: (-1) produceGEOSampleInfoTemplate.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) produceGEOSubmissionFile.Rd:23: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) produceMethylationGEOSubmissionFile.Rd:23: Escaped LaTeX specials: \_ \_ \_ \_
checkRd: (-1) seq2id.Rd:18: Escaped LaTeX specials: \_
* 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 75.938  5.448 119.190
getChipInfo      7.232  0.331  10.575
plotGammaFit     5.573  0.295   8.405
nuID2IlluminaID  5.355  0.036   7.799
MAplot-methods   5.299  0.079   7.417
targetID2nuID    5.168  0.030   7.722
probeID2nuID     5.164  0.031   7.543
nuID2probeID     5.086  0.036   7.504
nuID2targetID    5.054  0.031   7.632
gammaFitEM       4.297  0.301   6.291
methylationCall  4.154  0.292   6.391
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/lumi.Rcheck/00check.log’
for details.



Installation output

lumi.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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-class3.4060.0934.672
MAplot-methods5.2990.0797.417
addAnnotationInfo0.0920.0040.127
addControlData2lumi0.0010.0000.000
addNuID2lumi0.0010.0010.000
adjColorBias.quantile2.2160.0643.153
adjColorBias.ssn0.6140.0310.861
bgAdjust0.1220.0030.175
bgAdjustMethylation0.2560.0110.355
boxplot-MethyLumiM-methods0.8150.0171.131
boxplot-methods0.1390.0050.188
boxplotColorBias0.2100.0170.303
density-methods0.1350.0050.198
detectOutlier0.1360.0060.197
detectionCall0.2320.0080.327
estimateBeta0.3080.0100.453
estimateIntensity0.3310.0060.461
estimateLumiCV0.1510.0040.211
estimateM0.7780.0121.051
estimateMethylationBG0.2190.0060.291
example.lumi0.1140.0030.159
example.lumiMethy0.0910.0030.132
example.methyTitration0.2730.0070.371
gammaFitEM4.2970.3016.291
getChipInfo 7.232 0.33110.575
getControlData0.0020.0010.002
getControlProbe0.0010.0000.001
getControlType0.0010.0000.004
getNuIDMappingInfo1.7760.0922.619
hist-methods0.1720.0080.244
id2seq0.0010.0000.002
inverseVST0.8180.0241.165
is.nuID0.0010.0000.001
lumiB0.1350.0030.190
lumiExpresso0.3540.0090.516
lumiMethyB0.0980.0030.140
lumiMethyC1.7160.0562.587
lumiMethyN0.1300.0040.183
lumiMethyStatus 75.938 5.448119.190
lumiN0.7240.0461.044
lumiQ0.4210.0120.612
lumiR000
lumiR.batch000
lumiT0.4670.0150.665
methylationCall4.1540.2926.391
normalizeMethylation.quantile0.2560.0180.394
normalizeMethylation.ssn0.2220.0040.312
nuID2EntrezID1.6370.0322.350
nuID2IlluminaID5.3550.0367.799
nuID2RefSeqID1.5600.0212.333
nuID2probeID5.0860.0367.504
nuID2targetID5.0540.0317.632
pairs-methods1.2490.0442.019
plot-methods2.5630.0454.045
plotCDF0.2040.0080.323
plotColorBias1D0.2780.0070.452
plotColorBias2D0.2640.0060.397
plotControlData0.0010.0010.001
plotDensity0.1700.0050.262
plotGammaFit5.5730.2958.405
plotHousekeepingGene0.0010.0010.001
plotSampleRelation1.1570.0081.687
plotStringencyGene0.0010.0010.002
plotVST0.4490.0150.660
probeID2nuID5.1640.0317.543
produceGEOPlatformFile000
produceGEOSubmissionFile0.0010.0000.000
produceMethylationGEOSubmissionFile0.0010.0000.001
seq2id0.0000.0000.001
targetID2nuID5.1680.0307.722
vst0.3880.0090.596