Back to Multiple platform build/check report for BioC 3.17
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2023-02-01 11:05:47 -0500 (Wed, 01 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 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 1052/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.51.0  (landing page)
Lei Huang
Snapshot Date: 2023-01-31 14:00:20 -0500 (Tue, 31 Jan 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: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings lumi_2.51.0.tar.gz
StartedAt: 2023-01-31 21:30:53 -0500 (Tue, 31 Jan 2023)
EndedAt: 2023-01-31 21:37:37 -0500 (Tue, 31 Jan 2023)
EllapsedTime: 404.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: lumi.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:lumi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings lumi_2.51.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/lumi.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* 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 37.501  0.664  38.165
* checking PDF version of manual ... OK
* DONE

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



Installation output

lumi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL lumi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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-class2.0280.1242.152
MAplot-methods4.3670.0524.420
addAnnotationInfo0.0540.0000.054
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile1.6460.1801.825
adjColorBias.ssn0.3240.0280.352
bgAdjust0.0700.0030.073
bgAdjustMethylation0.1290.0090.137
boxplot-MethyLumiM-methods0.4140.0000.415
boxplot-methods0.0790.0040.082
boxplotColorBias0.1160.0040.121
density-methods0.0850.0000.084
detectOutlier0.0800.0030.083
detectionCall0.1360.0050.139
estimateBeta0.1440.0150.160
estimateIntensity0.1450.0230.170
estimateLumiCV0.0750.0120.086
estimateM0.3960.0040.400
estimateMethylationBG0.1060.0010.106
example.lumi0.0690.0000.069
example.lumiMethy0.0620.0000.061
example.methyTitration0.1650.0070.173
gammaFitEM1.9210.0051.926
getChipInfo3.7690.2954.141
getControlData0.0010.0000.001
getControlProbe0.0010.0000.001
getControlType0.0010.0000.001
getNuIDMappingInfo0.9550.0320.996
hist-methods0.1110.0000.110
id2seq0.0010.0000.001
inverseVST0.4370.0320.469
is.nuID000
lumiB0.0860.0000.086
lumiExpresso0.2100.0240.234
lumiMethyB0.0580.0040.062
lumiMethyC0.9430.0040.947
lumiMethyN0.080.000.08
lumiMethyStatus37.501 0.66438.165
lumiN0.3940.0080.402
lumiQ0.2430.0040.246
lumiR0.0010.0000.000
lumiR.batch0.0000.0000.001
lumiT0.3070.0000.308
methylationCall1.8480.0081.857
normalizeMethylation.quantile0.1480.0000.149
normalizeMethylation.ssn0.1170.0000.117
nuID2EntrezID0.7150.0080.722
nuID2IlluminaID3.1160.0203.136
nuID2RefSeqID2.2480.0842.332
nuID2probeID2.8630.0042.867
nuID2targetID2.8280.0082.836
pairs-methods0.7160.0200.737
plot-methods1.9060.0191.924
plotCDF0.1310.0080.140
plotColorBias1D0.1750.0040.178
plotColorBias2D0.150.000.15
plotControlData0.0000.0010.001
plotDensity0.1020.0050.107
plotGammaFit2.3070.0082.314
plotHousekeepingGene0.0010.0000.001
plotSampleRelation0.4140.0400.453
plotStringencyGene0.0010.0000.001
plotVST0.2960.0040.299
probeID2nuID2.7380.0282.766
produceGEOPlatformFile0.0000.0010.000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile000
seq2id000
targetID2nuID2.8340.0362.869
vst0.1640.0000.165