Lei Huang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 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 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:54 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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. |
| Package 1024/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| lumi 2.47.0 (landing page) Lei Huang
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: lumi |
| Version: 2.47.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lumi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lumi_2.47.0.tar.gz |
| StartedAt: 2022-03-17 19:27:49 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:34:03 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 373.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:lumi.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings lumi_2.47.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'lumi' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.5Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 3.6Mb
* 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 44.75 6 50.75
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
'D:/biocbuild/bbs-3.15-bioc/meat/lumi.Rcheck/00check.log'
for details.
lumi.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL lumi
###
##############################################################################
##############################################################################
* installing to library 'D:/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
converting help for package 'lumi'
finding HTML links ... done
IlluminaID2nuID html
LumiBatch-class html
MAplot-methods html
addAnnotationInfo html
addControlData2lumi html
addControlData2methyLumiM html
addNuID2lumi html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-lumi/00new/lumi/help/addNuId2lumi.html
adjColorBias.quantile html
adjColorBias.ssn html
asBigMatrix-methods html
beta2m html
bgAdjust html
bgAdjustMethylation html
boxplot-MethyLumiM-methods html
finding level-2 HTML links ... done
boxplot-methods html
boxplotColorBias html
colorBiasSummary html
density-methods html
detectOutlier html
detectionCall html
estimateBeta html
estimateIntensity html
estimateLumiCV html
estimateM html
estimateMethylationBG html
example.lumi html
example.lumiMethy html
example.methyTitration html
gammaFitEM html
getChipInfo html
getChrInfo html
getControlData html
getControlProbe html
getControlType html
getNuIDMappingInfo html
hist-methods html
id2seq html
importMethyIDAT html
inverseVST html
is.nuID html
lumi.package html
lumiB html
lumiExpresso html
lumiMethyB html
lumiMethyC html
lumiMethyN html
lumiMethyR html
lumiMethyStatus html
lumiN html
lumiQ html
lumiR html
lumiR.batch html
lumiT html
m2beta html
methylationCall html
monoSmu html
monoSpline html
normalizeMethylation.quantile html
normalizeMethylation.ssn html
nuID2EntrezID html
nuID2IlluminaID html
nuID2RefSeqID html
nuID2probeID html
nuID2targetID html
pairs-methods html
plot-methods html
plotCDF html
plotColorBias1D html
plotColorBias2D html
plotControlData html
plotDensity html
plotGammaFit html
plotHousekeepingGene html
plotSampleRelation html
plotStringencyGene html
plotVST html
probeID2nuID html
produceGEOPlatformFile html
produceGEOSampleInfoTemplate html
produceGEOSubmissionFile html
produceMethylationGEOSubmissionFile html
rankinvariant html
rsn html
seq2id html
smoothQuantileNormalization html
ssn html
targetID2nuID html
vst html
** 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)
Making 'packages.html' ... done
lumi.Rcheck/lumi-Ex.timings
| name | user | system | elapsed | |
| LumiBatch-class | 0.69 | 0.15 | 0.84 | |
| MAplot-methods | 3.19 | 0.08 | 3.26 | |
| addAnnotationInfo | 0.04 | 0.00 | 0.03 | |
| addControlData2lumi | 0 | 0 | 0 | |
| addNuID2lumi | 0 | 0 | 0 | |
| adjColorBias.quantile | 1.28 | 0.03 | 1.31 | |
| adjColorBias.ssn | 0.31 | 0.02 | 0.33 | |
| bgAdjust | 0.06 | 0.00 | 0.06 | |
| bgAdjustMethylation | 0.10 | 0.01 | 0.11 | |
| boxplot-MethyLumiM-methods | 0.39 | 0.02 | 0.41 | |
| boxplot-methods | 0.06 | 0.00 | 0.07 | |
| boxplotColorBias | 0.09 | 0.00 | 0.09 | |
| density-methods | 0.06 | 0.00 | 0.06 | |
| detectOutlier | 0.08 | 0.00 | 0.08 | |
| detectionCall | 0.1 | 0.0 | 0.1 | |
| estimateBeta | 0.11 | 0.00 | 0.11 | |
| estimateIntensity | 0.12 | 0.00 | 0.13 | |
| estimateLumiCV | 0.08 | 0.00 | 0.07 | |
| estimateM | 0.48 | 0.00 | 0.49 | |
| estimateMethylationBG | 0.10 | 0.00 | 0.09 | |
| example.lumi | 0.04 | 0.00 | 0.05 | |
| example.lumiMethy | 0.05 | 0.00 | 0.05 | |
| example.methyTitration | 0.16 | 0.00 | 0.15 | |
| gammaFitEM | 2.93 | 0.49 | 3.42 | |
| getChipInfo | 3.33 | 0.37 | 4.93 | |
| getControlData | 0 | 0 | 0 | |
| getControlProbe | 0 | 0 | 0 | |
| getControlType | 0 | 0 | 0 | |
| getNuIDMappingInfo | 0.64 | 0.08 | 0.81 | |
| hist-methods | 0.08 | 0.00 | 0.08 | |
| id2seq | 0 | 0 | 0 | |
| inverseVST | 0.34 | 0.01 | 0.36 | |
| is.nuID | 0 | 0 | 0 | |
| lumiB | 0.06 | 0.00 | 0.06 | |
| lumiExpresso | 0.16 | 0.00 | 0.16 | |
| lumiMethyB | 0.03 | 0.02 | 0.05 | |
| lumiMethyC | 0.67 | 0.05 | 0.72 | |
| lumiMethyN | 0.07 | 0.00 | 0.06 | |
| lumiMethyStatus | 44.75 | 6.00 | 50.75 | |
| lumiN | 0.35 | 0.00 | 0.36 | |
| lumiQ | 0.31 | 0.00 | 0.32 | |
| lumiR | 0 | 0 | 0 | |
| lumiR.batch | 0 | 0 | 0 | |
| lumiT | 0.28 | 0.03 | 0.31 | |
| methylationCall | 2.54 | 0.25 | 2.78 | |
| normalizeMethylation.quantile | 0.09 | 0.03 | 0.12 | |
| normalizeMethylation.ssn | 0.12 | 0.00 | 0.13 | |
| nuID2EntrezID | 0.66 | 0.01 | 0.67 | |
| nuID2IlluminaID | 2.78 | 0.04 | 2.81 | |
| nuID2RefSeqID | 0.69 | 0.00 | 0.69 | |
| nuID2probeID | 2.83 | 0.00 | 2.83 | |
| nuID2targetID | 3.01 | 0.03 | 3.05 | |
| pairs-methods | 0.63 | 0.06 | 0.68 | |
| plot-methods | 1.34 | 0.03 | 1.38 | |
| plotCDF | 0.16 | 0.02 | 0.17 | |
| plotColorBias1D | 0.26 | 0.01 | 0.28 | |
| plotColorBias2D | 0.14 | 0.00 | 0.14 | |
| plotControlData | 0 | 0 | 0 | |
| plotDensity | 0.1 | 0.0 | 0.1 | |
| plotGammaFit | 3.12 | 0.55 | 3.67 | |
| plotHousekeepingGene | 0 | 0 | 0 | |
| plotSampleRelation | 0.28 | 0.01 | 0.29 | |
| plotStringencyGene | 0 | 0 | 0 | |
| plotVST | 0.25 | 0.02 | 0.27 | |
| probeID2nuID | 2.43 | 0.03 | 2.45 | |
| produceGEOPlatformFile | 0 | 0 | 0 | |
| produceGEOSubmissionFile | 0 | 0 | 0 | |
| produceMethylationGEOSubmissionFile | 0 | 0 | 0 | |
| seq2id | 0 | 0 | 0 | |
| targetID2nuID | 2.40 | 0.05 | 2.46 | |
| vst | 0.13 | 0.00 | 0.12 | |