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BioC 3.0: CHECK report for lumi on oaxaca

This page was generated on 2015-04-10 10:02:23 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.18.0.tar.gz
StartedAt: 2015-04-10 00:53:20 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 01:04:44 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 683.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: lumi.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch lumi_2.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/lumi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.18.0’
* 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 ... [38s/41s] OK
* checking installed package size ... NOTE
  installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    5.2Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [236s/259s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
lumiMethyStatus    86.813  4.841 100.083
getNuIDMappingInfo 18.860  0.115  19.481
nuID2RefSeqID      14.188  0.061  15.889
nuID2EntrezID      12.116  0.061  13.420
getChipInfo         6.175  0.285  12.899
plotGammaFit        5.428  0.534   6.002
nuID2IlluminaID     5.761  0.143   6.479
nuID2targetID       5.597  0.136   6.287
methylationCall     5.131  0.205   5.950
probeID2nuID        5.055  0.146   5.226
nuID2probeID        5.022  0.132   5.827
targetID2nuID       4.952  0.136   5.385
gammaFitEM          4.666  0.319   5.202
* 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
  ‘/Users/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-class2.5830.0402.763
MAplot-methods4.7290.0514.952
addAnnotationInfo0.0660.0040.070
addControlData2lumi0.0000.0000.001
addNuID2lumi0.0000.0000.001
adjColorBias.quantile1.7680.0541.899
adjColorBias.ssn1.1430.0131.183
bgAdjust0.0970.0080.105
bgAdjustMethylation0.6770.0070.713
boxplot-MethyLumiM-methods1.2050.0091.227
boxplot-methods0.1350.0070.146
boxplotColorBias1.0820.0131.173
density-methods0.1100.0070.117
detectOutlier0.1260.0080.135
detectionCall0.1960.0120.208
estimateBeta0.1320.0050.137
estimateIntensity0.6020.0090.618
estimateLumiCV0.1370.0100.147
estimateM0.7870.0160.811
estimateMethylationBG0.6700.0040.675
example.lumi0.1010.0100.113
example.lumiMethy0.0660.0010.069
example.methyTitration0.2280.0120.241
gammaFitEM4.6660.3195.202
getChipInfo 6.175 0.28512.899
getControlData0.0050.0010.005
getControlProbe0.0040.0000.005
getControlType0.0040.0000.005
getNuIDMappingInfo18.860 0.11519.481
hist-methods0.1320.0070.139
id2seq0.0010.0000.002
inverseVST0.7650.0210.825
is.nuID0.0010.0000.001
lumiB0.1000.0050.105
lumiExpresso0.3630.0180.382
lumiMethyB0.0660.0030.069
lumiMethyC2.4330.0572.540
lumiMethyN0.0920.0020.094
lumiMethyStatus 86.813 4.841100.083
lumiN0.6740.0181.271
lumiQ0.3240.0160.378
lumiR0.0000.0000.001
lumiR.batch0.0000.0000.001
lumiT0.4650.0160.540
methylationCall5.1310.2055.950
normalizeMethylation.quantile0.2290.0060.261
normalizeMethylation.ssn0.2860.0040.326
nuID2EntrezID12.116 0.06113.420
nuID2IlluminaID5.7610.1436.479
nuID2RefSeqID14.188 0.06115.889
nuID2probeID5.0220.1325.827
nuID2targetID5.5970.1366.287
pairs-methods1.1060.0471.159
plot-methods2.4110.0422.480
plotCDF0.2210.0120.234
plotColorBias1D0.4170.0100.431
plotColorBias2D0.3340.0060.342
plotControlData0.0040.0000.005
plotDensity0.1430.0080.153
plotGammaFit5.4280.5346.002
plotHousekeepingGene0.0040.0010.005
plotSampleRelation0.9690.0100.981
plotStringencyGene0.0040.0010.005
plotVST0.4270.0150.447
probeID2nuID5.0550.1465.226
produceGEOPlatformFile0.0010.0000.001
produceGEOSubmissionFile0.0010.0010.000
produceMethylationGEOSubmissionFile0.0010.0000.001
seq2id0.0020.0000.001
targetID2nuID4.9520.1365.385
vst0.4390.0150.454