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BioC 3.0: CHECK report for lumi on zin1

This page was generated on 2015-04-10 09:37:36 -0700 (Fri, 10 Apr 2015).

Package 494/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lumi 2.18.0
Pan Du
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/lumi
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: lumi
Version: 2.18.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.18.0.tar.gz
StartedAt: 2015-04-10 01:30:45 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:39:45 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 540.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: lumi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings lumi_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/lumi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ‘2.18.0’
* 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 ... [34s/37s] OK
* checking installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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 ':::' import not declared from: ‘bigmemoryExtras’
'library' or 'require' call to ‘vsn’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addAnnotationInfo: no visible global function definition for ‘fData’
addAnnotationInfo: no visible global function definition for ‘keys’
addAnnotationInfo: no visible global function definition for ‘fData<-’
addNuID2lumi: no visible global function definition for ‘notes<-’
adjColorBias.quantile: no visible global function definition for
  ‘assayDataElementNames’
adjColorBias.quantile: no visible global function definition for
  ‘storageMode<-’
adjColorBias.quantile: no visible global function definition for
  ‘assayDataElement’
adjColorBias.quantile: no visible global function definition for
  ‘assayDataElement<-’
adjColorBias.ssn: no visible global function definition for
  ‘assayDataElementNames’
adjColorBias.ssn: no visible global function definition for
  ‘storageMode<-’
adjColorBias.ssn: no visible global function definition for
  ‘assayDataElement’
adjColorBias.ssn: no visible global function definition for
  ‘assayDataElement<-’
bgAdjustMethylation: no visible global function definition for
  ‘assayDataElementNames’
boxplotColorBias: no visible global function definition for
  ‘assayDataElementNames’
boxplotColorBias: no visible global function definition for
  ‘assayDataElement’
colorBiasSummary: no visible global function definition for
  ‘assayDataElementNames’
colorBiasSummary: no visible global function definition for
  ‘assayDataElement’
detectionCall: no visible global function definition for
  ‘assayDataValidMembers’
detectionCall: no visible global function definition for
  ‘assayDataElement’
estimateBeta: no visible global function definition for
  ‘assayDataElementNames’
estimateBeta: no visible global function definition for
  ‘assayDataElement’
estimateBeta: no visible global function definition for
  ‘assayDataElement<-’
estimateIntensity: no visible global function definition for
  ‘assayDataElementNames’
estimateIntensity: no visible global function definition for
  ‘assayDataElement’
estimateIntensity: no visible global function definition for
  ‘assayDataElement<-’
estimateM: no visible global function definition for
  ‘assayDataElementNames’
estimateM: no visible global function definition for ‘assayDataElement’
estimateM: no visible global function definition for
  ‘assayDataElement<-’
estimateMethylationBG: no visible global function definition for
  ‘assayDataElement’
estimateMethylationBG: no visible global function definition for
  ‘assayDataElementNames’
getChrInfo: no visible global function definition for ‘fData’
importMethyIDAT: no visible global function definition for
  ‘assayDataElementNames’
importMethyIDAT: no visible global function definition for
  ‘assayDataElement’
lumiMethyB: no visible global function definition for
  ‘assayDataElement’
lumiMethyC: no visible global function definition for
  ‘assayDataElement’
lumiMethyN: no visible global function definition for
  ‘assayDataElement’
lumiQ: no visible global function definition for ‘rowMin’
lumiR: no visible global function definition for ‘notes<-’
normalizeMethylation.quantile: no visible global function definition
  for ‘assayDataElementNames’
normalizeMethylation.quantile: no visible global function definition
  for ‘storageMode<-’
normalizeMethylation.quantile: no visible global function definition
  for ‘assayDataElement’
normalizeMethylation.quantile: no visible global function definition
  for ‘assayDataElement<-’
normalizeMethylation.ssn: no visible global function definition for
  ‘assayDataElementNames’
normalizeMethylation.ssn: no visible global function definition for
  ‘storageMode<-’
normalizeMethylation.ssn: no visible global function definition for
  ‘assayDataElement’
normalizeMethylation.ssn: no visible global function definition for
  ‘assayDataElement<-’
plotCDF: no visible global function definition for ‘rowMin’
plotColorBias1D: no visible global function definition for
  ‘assayDataElementNames’
plotColorBias1D: no visible global function definition for
  ‘assayDataElement’
plotColorBias2D: no visible global function definition for
  ‘assayDataElementNames’
plotColorBias2D: no visible global function definition for
  ‘assayDataElement’
plotControlData: no visible global function definition for
  ‘assayDataElement’
beadNum,ExpressionSet: no visible global function definition for
  ‘assayDataElementNames’
beadNum,ExpressionSet: no visible global function definition for
  ‘assayDataElement’
beadNum<-,ExpressionSet: no visible global function definition for
  ‘storageMode<-’
beadNum<-,ExpressionSet: no visible global function definition for
  ‘assayDataElementReplace’
combine,LumiBatch-LumiBatch: no visible global function definition for
  ‘protocolData<-’
combine,LumiBatch-LumiBatch: no visible global function definition for
  ‘protocolData’
detection,ExpressionSet: no visible global function definition for
  ‘assayDataElementNames’
detection,ExpressionSet: no visible global function definition for
  ‘assayDataElement’
detection<-,ExpressionSet: no visible global function definition for
  ‘storageMode<-’
detection<-,ExpressionSet: no visible global function definition for
  ‘assayDataElementReplace’
se.exprs,ExpressionSet: no visible global function definition for
  ‘assayDataElementNames’
se.exprs,ExpressionSet: no visible global function definition for
  ‘assayDataElement’
se.exprs<-,ExpressionSet: no visible global function definition for
  ‘storageMode<-’
se.exprs<-,ExpressionSet: no visible global function definition for
  ‘assayDataElementReplace’
* checking Rd files ... NOTE
prepare_Rd: getChrInfo.Rd:23-25: Dropping empty section \details
prepare_Rd: getChrInfo.Rd:29-31: Dropping empty section \references
prepare_Rd: getChrInfo.Rd:38-40: Dropping empty section \seealso
prepare_Rd: getChrInfo.Rd:41-44: Dropping empty section \examples
prepare_Rd: importMethyIDAT.Rd:39-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘bigmemoryExtras’, ‘hdrcde’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [191s/195s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lumiMethyStatus    88.545  0.000  89.220
getNuIDMappingInfo  7.292  0.032   7.490
nuID2RefSeqID       6.785  0.000   6.819
nuID2EntrezID       6.540  0.016   6.570
methylationCall     5.357  0.008   5.549
plotGammaFit        5.280  0.004   5.297
getChipInfo         5.112  0.136   6.160
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

WARNING: There was 1 warning.
NOTE: There were 5 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/lumi.Rcheck/00check.log’
for details.

lumi.Rcheck/00install.out:

* installing *source* package ‘lumi’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lumi)

lumi.Rcheck/lumi-Ex.timings:

nameusersystemelapsed
LumiBatch-class2.0610.0322.095
MAplot-methods4.6440.0084.660
addAnnotationInfo0.0560.0000.055
addControlData2lumi0.0040.0000.000
addNuID2lumi0.0000.0000.001
adjColorBias.quantile1.8520.0081.874
adjColorBias.ssn0.9480.0120.963
bgAdjust0.0760.0040.081
bgAdjustMethylation0.2280.0000.229
boxplot-MethyLumiM-methods0.9600.0000.962
boxplot-methods0.1080.0000.106
boxplotColorBias0.5760.0000.578
density-methods0.1000.0000.099
detectOutlier0.1000.0000.101
detectionCall0.5400.0000.541
estimateBeta0.1200.0000.118
estimateIntensity0.1760.0000.176
estimateLumiCV0.1120.0040.116
estimateM0.6040.0040.608
estimateMethylationBG0.5520.0000.553
example.lumi0.0720.0040.079
example.lumiMethy0.0560.0000.056
example.methyTitration0.1800.0040.184
gammaFitEM4.6730.0004.766
getChipInfo5.1120.1366.160
getControlData0.0040.0000.004
getControlProbe0.0040.0000.004
getControlType0.0040.0000.003
getNuIDMappingInfo7.2920.0327.490
hist-methods0.120.000.12
id2seq0.0000.0000.001
inverseVST0.5760.0080.601
is.nuID0.0000.0000.001
lumiB0.0840.0040.086
lumiExpresso0.3330.0120.362
lumiMethyB0.0560.0000.057
lumiMethyC1.9640.0001.968
lumiMethyN0.0800.0000.108
lumiMethyStatus88.545 0.00089.220
lumiN0.6240.0120.698
lumiQ0.2960.0120.312
lumiR000
lumiR.batch000
lumiT0.4560.0000.460
methylationCall5.3570.0085.549
normalizeMethylation.quantile0.2120.0040.217
normalizeMethylation.ssn0.2360.0000.237
nuID2EntrezID6.5400.0166.570
nuID2IlluminaID4.3440.0204.521
nuID2RefSeqID6.7850.0006.819
nuID2probeID3.9360.0163.973
nuID2targetID4.2680.0164.342
pairs-methods1.0840.0081.275
plot-methods2.2680.0282.329
plotCDF0.2000.0080.210
plotColorBias1D0.3600.0040.367
plotColorBias2D0.280.000.28
plotControlData0.0040.0000.005
plotDensity0.1330.0040.137
plotGammaFit5.2800.0045.297
plotHousekeepingGene0.0040.0000.003
plotSampleRelation0.8200.0080.831
plotStringencyGene0.0000.0000.003
plotVST0.3760.0000.377
probeID2nuID3.7880.0203.815
produceGEOPlatformFile0.0040.0000.001
produceGEOSubmissionFile0.0000.0000.001
produceMethylationGEOSubmissionFile0.0040.0000.000
seq2id0.0000.0000.001
targetID2nuID3.6840.0123.710
vst0.3640.0000.365