Lei Huang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/lumi |
| Branch: RELEASE_3_11 |
| Last Commit: 82db06c |
| Last Changed Date: 2020-04-27 14:14:29 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:58 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE lumi PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 961/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| lumi 2.40.0 Lei Huang
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: lumi |
| Version: 2.40.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/lumi_2.40.0.tar.gz && rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL lumi_2.40.0.zip && rm lumi_2.40.0.tar.gz lumi_2.40.0.zip |
| StartedAt: 2020-10-16 19:12:50 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 19:14:51 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 121.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/lumi_2.40.0.tar.gz && rm -rf lumi.buildbin-libdir && mkdir lumi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=lumi.buildbin-libdir lumi_2.40.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL lumi_2.40.0.zip && rm lumi_2.40.0.tar.gz lumi_2.40.0.zip
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install for i386
* 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
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:44: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:46: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:83: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:84: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:85: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:86: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:103: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:104: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:104: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:106: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:113: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/LumiBatch-class.Rd:113: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
MAplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/MAplot-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
addAnnotationInfo html
addControlData2lumi html
addControlData2methyLumiM html
addNuID2lumi html
adjColorBias.quantile html
adjColorBias.ssn html
asBigMatrix-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/asBigMatrix-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
beta2m html
bgAdjust html
bgAdjustMethylation html
boxplot-MethyLumiM-methods html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/boxplot-MethyLumiM-methods.Rd:16: file link 'bwplot' in package 'lattice' does not exist and so has been treated as a topic
boxplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/boxplot-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
boxplotColorBias html
colorBiasSummary html
density-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/density-methods.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
detectOutlier html
detectionCall html
estimateBeta html
estimateIntensity html
estimateLumiCV html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/estimateLumiCV.Rd:17: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
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-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/getControlType.Rd:20: file link 'controlTypes' in package 'methylumi' does not exist and so has been treated as a topic
getNuIDMappingInfo html
hist-methods html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/hist-methods.Rd:15: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
id2seq html
importMethyIDAT html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/importMethyIDAT.Rd:7: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/importMethyIDAT.Rd:20: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/importMethyIDAT.Rd:23: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/importMethyIDAT.Rd:37: file link 'lumIDAT' in package 'methylumi' does not exist and so has been treated as a topic
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-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/lumiN.Rd:19: missing file link 'vsn'
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-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/pairs-methods.Rd:16: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
plot-methods html
plotCDF html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotCDF.Rd:17: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotCDF.Rd:29: file link 'plot.ecdf' in package 'stats' does not exist and so has been treated as a topic
plotColorBias1D html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotColorBias1D.Rd:21: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotColorBias2D html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotColorBias2D.Rd:24: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotControlData html
plotDensity html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotDensity.Rd:14: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
plotGammaFit html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotGammaFit.Rd:22: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
plotHousekeepingGene html
plotSampleRelation html
plotStringencyGene html
plotVST html
Rd warning: C:/Users/biocbuild/bbs-3.11-bioc/tmpdir/RtmpIpk90B/R.INSTALL2ea42ff516a5/lumi/man/plotVST.Rd:17: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
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
install for x64
* installing *source* package 'lumi' ...
** testing if installed package can be loaded
No methods found in package 'RSQLite' for request: 'dbListFields' when loading 'lumi'
* MD5 sums
packaged installation of 'lumi' as lumi_2.40.0.zip
* DONE (lumi)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'lumi' successfully unpacked and MD5 sums checked