Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

This page was generated on 2022-06-24 12:07:41 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 1046/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.48.0  (landing page)
Lei Huang
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/lumi
git_branch: RELEASE_3_15
git_last_commit: 1f988ff
git_last_commit_date: 2022-04-26 10:59:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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: 2.48.0
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_2.48.0.tar.gz
StartedAt: 2022-06-24 04:34:08 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:47:22 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 794.8 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_2.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.48.0’
* 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 89.563  8.073 101.030
getChipInfo      7.126  0.309   7.564
plotGammaFit     6.159  0.642   6.884
nuID2IlluminaID  6.513  0.046   6.904
gammaFitEM       5.172  0.533   5.824
MAplot-methods   5.337  0.075   5.458
methylationCall  5.073  0.334   5.689
probeID2nuID     5.185  0.031   5.350
targetID2nuID    5.081  0.027   5.326
nuID2targetID    5.023  0.024   5.113
nuID2probeID     4.935  0.021   5.077
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs
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-class2.2250.0872.327
MAplot-methods5.3370.0755.458
addAnnotationInfo0.1040.0040.108
addControlData2lumi000
addNuID2lumi000
adjColorBias.quantile2.1720.1062.293
adjColorBias.ssn1.6510.0371.708
bgAdjust0.1250.0020.127
bgAdjustMethylation0.2640.0110.280
boxplot-MethyLumiM-methods0.8330.0270.874
boxplot-methods0.1400.0040.145
boxplotColorBias0.2060.0090.220
density-methods0.1340.0030.145
detectOutlier0.1380.0040.144
detectionCall0.2560.0140.275
estimateBeta0.2960.0060.308
estimateIntensity0.3400.0060.349
estimateLumiCV0.1450.0030.151
estimateM0.7820.0150.809
estimateMethylationBG0.2380.0110.252
example.lumi0.1160.0030.124
example.lumiMethy0.1010.0030.104
example.methyTitration0.2710.0070.283
gammaFitEM5.1720.5335.824
getChipInfo7.1260.3097.564
getControlData0.0020.0000.002
getControlProbe0.0010.0000.002
getControlType0.0010.0000.002
getNuIDMappingInfo1.6420.0741.760
hist-methods0.1710.0040.176
id2seq0.0010.0000.002
inverseVST0.8340.0320.874
is.nuID0.0010.0000.001
lumiB0.1370.0030.142
lumiExpresso0.3540.0090.365
lumiMethyB0.1090.0030.112
lumiMethyC1.5460.1031.673
lumiMethyN0.1390.0030.142
lumiMethyStatus 89.563 8.073101.030
lumiN0.6810.0150.730
lumiQ0.4520.0330.510
lumiR000
lumiR.batch0.0000.0010.000
lumiT0.4690.0150.517
methylationCall5.0730.3345.689
normalizeMethylation.quantile0.2800.0150.311
normalizeMethylation.ssn0.2410.0030.255
nuID2EntrezID1.6320.0321.751
nuID2IlluminaID6.5130.0466.904
nuID2RefSeqID1.7430.0301.840
nuID2probeID4.9350.0215.077
nuID2targetID5.0230.0245.113
pairs-methods1.1990.0431.251
plot-methods2.5400.0412.618
plotCDF0.1970.0070.206
plotColorBias1D0.3810.0090.393
plotColorBias2D0.2600.0060.268
plotControlData0.0020.0000.002
plotDensity0.1750.0040.180
plotGammaFit6.1590.6426.884
plotHousekeepingGene0.0020.0000.002
plotSampleRelation1.1430.0051.154
plotStringencyGene0.0010.0010.002
plotVST0.4590.0140.480
probeID2nuID5.1850.0315.350
produceGEOPlatformFile000
produceGEOSubmissionFile000
produceMethylationGEOSubmissionFile0.0000.0000.001
seq2id0.0010.0000.001
targetID2nuID5.0810.0275.326
vst0.3860.0070.415