Pan Du
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: RELEASE_3_6 |
| Last Commit: de64da0 |
| Last Changed Date: 2017-10-30 12:39:19 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:18:32 -0400 (Thu, 12 Apr 2018).
| Package 763/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lumi 2.30.0 Pan Du
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: lumi |
| Version: 2.30.0 |
| Command: rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.30.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.30.0.tar.gz |
| StartedAt: 2018-04-12 01:04:30 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:15:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 661.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: lumi.Rcheck |
| Warnings: 4 |
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###
### Running command:
###
### rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.30.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '2.30.0'
* 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 ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:44: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:46: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:83: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:84: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:85: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:86: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:103: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:104: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:104: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:106: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:113: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:113: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/MAplot-methods.Rd:16: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/asBigMatrix-methods.Rd:15: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/boxplot-MethyLumiM-methods.Rd:16: missing file link 'bwplot'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/boxplot-methods.Rd:15: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/density-methods.Rd:17: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/getControlType.Rd:20: missing file link 'controlTypes'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/hist-methods.Rd:15: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:7: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:20: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:23: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:37: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/lumiN.Rd:19: file link 'vsn' in package 'vsn' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/pairs-methods.Rd:16: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/plotCDF.Rd:17: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/plotCDF.Rd:29: missing file link 'plot.ecdf'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/plotDensity.Rd:14: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck/00install.out' for details.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages unavailable to check Rd xrefs: 'bigmemoryExtras', 'hdrcde'
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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 72.32 0.00 72.31
getChipInfo 6.59 0.15 21.06
MAplot-methods 5.64 0.02 5.66
nuID2IlluminaID 5.34 0.01 5.36
methylationCall 5.22 0.02 5.24
nuID2probeID 5.13 0.03 5.15
targetID2nuID 5.08 0.00 5.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 72.87 0.01 72.90
nuID2IlluminaID 5.26 0.04 5.29
* checking PDF version of manual ... OK
* DONE
Status: 4 WARNINGs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/lumi.Rcheck/00check.log'
for details.
lumi.Rcheck/00install.out
install for i386
* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'lumi'
finding HTML links ... done
IlluminaID2nuID html
LumiBatch-class html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:44: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:46: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:83: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:84: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:85: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:86: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:103: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:104: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:104: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:106: missing file link 'eSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:113: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/LumiBatch-class.Rd:113: missing file link 'eSet'
MAplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/MAplot-methods.Rd:16: missing file link 'ExpressionSet'
addAnnotationInfo html
addControlData2lumi html
addControlData2methyLumiM html
addNuID2lumi html
adjColorBias.quantile html
adjColorBias.ssn html
asBigMatrix-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/asBigMatrix-methods.Rd:15: missing file link 'ExpressionSet'
beta2m html
bgAdjust html
bgAdjustMethylation html
boxplot-MethyLumiM-methods html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/boxplot-MethyLumiM-methods.Rd:16: missing file link 'bwplot'
boxplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/boxplot-methods.Rd:15: missing file link 'ExpressionSet'
boxplotColorBias html
colorBiasSummary html
density-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/density-methods.Rd:17: missing file link 'ExpressionSet'
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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/getControlType.Rd:20: missing file link 'controlTypes'
getNuIDMappingInfo html
hist-methods html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/hist-methods.Rd:15: missing file link 'ExpressionSet'
id2seq html
importMethyIDAT html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:7: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:20: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:23: missing file link 'lumIDAT'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/importMethyIDAT.Rd:37: missing file link 'lumIDAT'
inverseVST html
is.nuID html
lumi.package html
lumiB html
lumiExpresso html
lumiMethyB html
lumiMethyC html
lumiMethyN html
lumiMethyR html
lumiMethyStatus html
lumiN html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/lumiN.Rd:19: file link 'vsn' in package 'vsn' does not exist and so has been treated as a topic
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
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/pairs-methods.Rd:16: missing file link 'ExpressionSet'
plot-methods html
plotCDF html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/plotCDF.Rd:17: missing file link 'ExpressionSet'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/plotCDF.Rd:29: missing file link 'plot.ecdf'
plotColorBias1D html
plotColorBias2D html
plotControlData html
plotDensity html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpEJix2w/R.INSTALL10a05b374d63/lumi/man/plotDensity.Rd:14: missing file link 'ExpressionSet'
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
In R CMD INSTALL
install for x64
* installing *source* package 'lumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lumi' as lumi_2.30.0.zip
* DONE (lumi)
In R CMD INSTALL
In R CMD INSTALL
|
lumi.Rcheck/examples_i386/lumi-Ex.timings
|
lumi.Rcheck/examples_x64/lumi-Ex.timings
|