lumi 2.22.0
Pan Du
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/lumi | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| windows1.bioconductor.org | Windows Server 2012 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 | |
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### Running command:
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### rm -rf lumi.buildbin-libdir lumi.Rcheck && mkdir lumi.buildbin-libdir lumi.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lumi.buildbin-libdir lumi_2.22.0.tar.gz >lumi.Rcheck\00install.out 2>&1 && cp lumi.Rcheck\00install.out lumi-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=lumi.buildbin-libdir --install="check:lumi-install.out" --force-multiarch --no-vignettes --timings lumi_2.22.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/lumi.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '2.22.0'
* 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:
Warning: bad markup (extra space?) at lumiMethyR.Rd:18:16
Warning: bad markup (extra space?) at lumiMethyR.Rd:19:28
Warning: bad markup (extra space?) at lumiMethyR.Rd:20:13
See 'C:/biocbld/bbs-3.2-bioc/meat/lumi.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 9.3Mb
sub-directories of 1Mb or more:
data 3.6Mb
doc 5.0Mb
* 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
* 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 ':::' 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'
MAplot,ExpressionSet : .local: no visible global function definition
for 'rowMin'
asBigMatrix,ExpressionSet : .local: no visible global function
definition for 'assayDataElementNames'
asBigMatrix,ExpressionSet : .local: no visible global function
definition for 'assayDataElement'
asBigMatrix,ExpressionSet : .local: no visible global function
definition for 'assayDataElement<-'
asBigMatrix,ExpressionSet : .local: no visible global function
definition for 'AnnotatedDataFrame'
asBigMatrix,ExpressionSet : .local: no visible global function
definition for 'fData'
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'
boxplot,ExpressionSet : .local: no visible global function definition
for 'description'
boxplot,ExpressionSet : .local: no visible global function definition
for 'rowMin'
boxplot,MethyLumiM : .local: no visible global function definition for
'description'
combine,LumiBatch-LumiBatch: no visible global function definition for
'protocolData<-'
combine,LumiBatch-LumiBatch: no visible global function definition for
'protocolData'
density,ExpressionSet : .local: no visible global function definition
for 'rowMin'
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'
pairs,ExpressionSet : .local: no visible global function definition for
'rowMin'
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 ... WARNING
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
prepare_Rd: bad markup (extra space?) at lumiMethyR.Rd:18:16
prepare_Rd: bad markup (extra space?) at lumiMethyR.Rd:19:28
prepare_Rd: bad markup (extra space?) at lumiMethyR.Rd:20:13
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'bigmemoryExtras'
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'lumiMethyR':
'qcfile' 'sampleDescriptions' 'sep'
* 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 ...
** running examples for arch 'i386' ... [142s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 63.83 0.0 63.84
getChipInfo 3.91 0.2 13.60
** running examples for arch 'x64' ... [139s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
lumiMethyStatus 65.7 0 65.71
* 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
Status: 4 WARNINGs, 4 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/lumi.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
Warning: bad markup (extra space?) at lumiMethyR.Rd:18:16
Warning: bad markup (extra space?) at lumiMethyR.Rd:19:28
Warning: bad markup (extra space?) at lumiMethyR.Rd:20:13
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'lumi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lumi' as lumi_2.22.0.zip
* DONE (lumi)