Package: affyPara

Version: 1.42.0

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyPara.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings affyPara_1.42.0.tar.gz

StartedAt: 2019-04-13 00:26:22 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:28:28 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 126.1 seconds

RetCode: 0

Status:  OK

CheckDir: affyPara.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:affyPara.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings affyPara_1.42.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/affyPara.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affyPara/DESCRIPTION' ... OK
* this is package 'affyPara' version '1.42.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 'affyPara' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'affy'
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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  'affy' 'aplpack' 'snow' 'vsn'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'affyio' 'aplpack' 'methods' 'snow' 'vsn'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'vsn:::isSmall' 'vsn:::optimparNames' 'vsn:::pstartHeuristic'
  'vsn:::vsnLTS'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
.doSummarizationPara: no visible global function definition for
  'clusterCall'
.doSummarizationPara: no visible global function definition for 'new'
.doSummarizationPara: no visible global function definition for
  'phenoData'
.doSummarizationPara: no visible global function definition for
  'experimentData'
.doSummarizationPara: no visible global function definition for
  'annotation'
.doSummarizationPara: no visible global function definition for
  'getMethod'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
.permArrays: no visible global function definition for 'clusterCall'
.permMatrix: no visible global function definition for 'clusterCall'
.resetABSF: no visible global function definition for 'exprs<-'
.resetABSF: no visible global function definition for 'sampleNames<-'
.rowMeansPara: no visible global function definition for 'clusterCall'
.rowVPara: no visible global function definition for 'clusterCall'
MAplotPara: no visible global function definition for 'checkCluster'
MAplotPara: no visible global function definition for 'clusterApply'
MAplotPara: no visible global function definition for 'clusterCall'
bgCorrectPara: no visible global function definition for 'new'
bgCorrectPara: no visible global function definition for 'checkCluster'
bgCorrectPara: no visible global function definition for 'clusterApply'
bgCorrectPara: no visible global function definition for 'clusterCall'
bgCorrectPara: no visible global function definition for 'pData'
boxplotPara: no visible global function definition for 'checkCluster'
boxplotPara: no visible global function definition for 'clusterApply'
boxplotPara: no visible global function definition for 'clusterCall'
boxplotParagLimits: no visible global function definition for 'par'
boxplotParagMdMnDef: no visible binding for global variable 'median'
boxplotParagMdMnDef: no visible global function definition for 'median'
boxplotParagMedIQR: no visible global function definition for 'par'
boxplotParagMedIQR: no visible global function definition for 'bxp'
boxplotParagMedIQR: no visible global function definition for 'abline'
boxplotParagMedIQR: no visible global function definition for 'bagplot'
boxplotParagMedIQR: no visible global function definition for 'title'
boxplotParagMedIQR: no visible global function definition for 'text'
computeExprSetPara: no visible global function definition for 'new'
computeExprSetPara: no visible global function definition for
  'checkCluster'
computeExprSetPara: no visible global function definition for
  'clusterApply'
distributeFiles: no visible global function definition for
  'checkCluster'
distributeFiles: no visible global function definition for
  'clusterEvalQ'
distributeFiles: no visible global function definition for
  'clusterCall'
distributeFiles: no visible global function definition for
  'clusterSplit'
drawHistDiff: no visible global function definition for 'abline'
drawHistDiff: no visible global function definition for 'text'
drawMAplot: no visible global function definition for 'frame'
drawMAplot: no visible global function definition for 'par'
drawnBxp: no visible global function definition for 'bxp'
drawnBxp: no visible global function definition for 'abline'
drawnBxp: no visible global function definition for 'legend'
getBoxplot: no visible global function definition for 'par'
getBoxplot: no visible global function definition for 'abline'
getValuesChips: no visible global function definition for 'IQR'
getValuesChips: no visible global function definition for 'median'
getValuesChips: no visible global function definition for 'loess'
getValuesChips: no visible global function definition for 'approx'
grad_loglikPara: no visible global function definition for
  'clusterCall'
justvsnPara: no visible global function definition for 'clusterCall'
logikPara: no visible global function definition for 'clusterCall'
mergeAffyBatches: no visible global function definition for 'phenoData'
mergeAffyBatches: no visible global function definition for 'new'
mergeAffyBatches: no visible global function definition for 'notes<-'
mergeAffyBatches: no visible global function definition for 'pData<-'
mergeAffyBatches: no visible global function definition for 'pData'
mergeAffyBatches: no visible global function definition for 'exprs<-'
mergeAffyBatches: no visible global function definition for
  'phenoData<-'
mergeAffyBatches: no visible global function definition for
  'experimentData<-'
normalizeAffyBatchConstantPara: no visible global function definition
  for 'new'
normalizeAffyBatchConstantPara: no visible global function definition
  for 'checkCluster'
normalizeAffyBatchConstantPara: no visible global function definition
  for 'clusterApply'
normalizeAffyBatchConstantPara: no visible global function definition
  for 'clusterCall'
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for 'new'
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for 'checkCluster'
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for 'clusterApply'
normalizeAffyBatchInvariantsetPara: no visible global function
  definition for 'clusterCall'
normalizeAffyBatchLoessIterPara: no visible global function definition
  for 'new'
normalizeAffyBatchLoessIterPara: no visible global function definition
  for 'checkCluster'
normalizeAffyBatchLoessIterPara: no visible global function definition
  for 'clusterApply'
normalizeAffyBatchLoessIterPara: no visible global function definition
  for 'clusterCall'
normalizeAffyBatchLoessPara: no visible global function definition for
  'new'
normalizeAffyBatchLoessPara: no visible global function definition for
  'checkCluster'
normalizeAffyBatchLoessPara: no visible global function definition for
  'clusterApply'
normalizeAffyBatchLoessPara: no visible global function definition for
  'clusterCall'
normalizeAffyBatchQuantilesPara: no visible global function definition
  for 'new'
normalizeAffyBatchQuantilesPara: no visible global function definition
  for 'checkCluster'
normalizeAffyBatchQuantilesPara: no visible global function definition
  for 'clusterApply'
normalizeAffyBatchQuantilesPara: no visible global function definition
  for 'clusterCall'
normalizeConstantPara: no visible global function definition for
  'clusterCall'
normalizeInvariantsetPara: no visible global function definition for
  'clusterCall'
normalizeInvariantsetPara: no visible global function definition for
  'median'
normalizeInvariantsetPara: no visible binding for global variable
  'median'
normalizeInvariantsetPara: no visible global function definition for
  'rowMedians'
normalizeInvariantsetParaSF2: no visible global function definition for
  'approx'
normalizeLoessIterPara: no visible global function definition for
  'clusterCall'
normalizeLoessIterParaSFnodes: no visible global function definition
  for 'loess'
normalizeLoessIterParaSFnodes: no visible global function definition
  for 'predict'
normalizeLoessPara: no visible global function definition for
  'clusterCall'
normalizeLoessParaSFbetNodes: no visible global function definition for
  'loess'
normalizeLoessParaSFbetNodes: no visible global function definition for
  'predict'
normalizeLoessParaSFnodes: no visible global function definition for
  'loess'
normalizeLoessParaSFnodes: no visible global function definition for
  'predict'
normalizeQuantilesPara: no visible global function definition for
  'clusterCall'
preproPara: no visible global function definition for 'new'
preproPara: no visible global function definition for 'checkCluster'
preproPara: no visible global function definition for 'clusterApply'
preproPara: no visible global function definition for 'clusterCall'
read.affybatchPara: no visible global function definition for 'new'
read.affybatchPara: no visible global function definition for
  'checkCluster'
read.affybatchPara: no visible global function definition for
  'clusterApply'
read.affybatchPara: no visible global function definition for
  'clusterCall'
read.affybatchPara: no visible global function definition for
  'phenoData<-'
read.affybatchPara: no visible global function definition for 'notes<-'
removeDistributedFiles: no visible global function definition for
  'checkCluster'
removeDistributedFiles: no visible global function definition for
  'clusterEvalQ'
removeDistributedFiles: no visible global function definition for
  'clusterCall'
rmaPara: no visible global function definition for 'new'
setupPara: no visible global function definition for 'clusterCall'
splitAffyBatch: no visible global function definition for
  'splitIndices'
splitFileVector: no visible global function definition for
  'splitIndices'
splitMatrix: no visible global function definition for 'splitCols'
stopCluster: no visible global function definition for 'checkCluster'
vsn2Para: no visible global function definition for 'new'
vsn2Para: no visible global function definition for 'checkCluster'
vsn2Para: no visible global function definition for 'clusterApply'
vsn2Para: no visible global function definition for 'clusterCall'
vsn2_optimPara: no visible global function definition for 'optim'
vsn2trsfPara: no visible global function definition for 'clusterCall'
vsnColumnByColumnPara: no visible global function definition for
  'clusterCall'
vsnColumnByColumnPara: no visible global function definition for 'new'
vsnColumnByColumnParaSF: no visible global function definition for
  'new'
vsnColumnByColumnParaSF: no visible global function definition for
  'coefficients'
vsnLTSPara: no visible global function definition for 'clusterCall'
vsnLTSPara: no visible global function definition for 'coefficients'
vsnLTSPara: no visible binding for global variable 'quantile'
vsnMLPara: no visible global function definition for 'new'
vsnMLPara: no visible global function definition for 'coefficients'
vsnMatrixPara: no visible global function definition for 'new'
vsnMatrixPara: no visible global function definition for 'coefficients'
vsnMatrixPara: no visible global function definition for
  'scalingFactorTransformation'
vsnMatrixPara: no visible global function definition for 'validObject'
vsnSamplePara: no visible global function definition for 'clusterCall'
vsnrmaPara: no visible global function definition for 'new'
vsnrmaPara: no visible global function definition for 'checkCluster'
vsnrmaPara: no visible global function definition for 'clusterApply'
vsnrmaPara: no visible global function definition for 'clusterCall'
Undefined global functions or variables:
  IQR abline addVigs2WinMenu annotation approx bagplot bxp checkCluster
  clusterApply clusterCall clusterEvalQ clusterSplit coefficients
  experimentData experimentData<- exprs<- frame getMethod legend loess
  median new notes<- optim pData pData<- par phenoData phenoData<-
  predict quantile rowMedians sampleNames<- scalingFactorTransformation
  splitCols splitIndices text title validObject
Consider adding
  importFrom("graphics", "abline", "bxp", "frame", "legend", "par",
             "text", "title")
  importFrom("methods", "getMethod", "new", "validObject")
  importFrom("stats", "IQR", "approx", "coefficients", "loess", "median",
             "optim", "predict", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/affyPara.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/affyPara_1.42.0.tar.gz && rm -rf affyPara.buildbin-libdir && mkdir affyPara.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=affyPara.buildbin-libdir affyPara_1.42.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL affyPara_1.42.0.zip && rm affyPara_1.42.0.tar.gz affyPara_1.42.0.zip
###
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install for i386

* installing *source* package 'affyPara' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'affyPara'
    finding HTML links ... done
    MAplotPara                              html  
    bgcPara                                 html  
    boxplotPara                             html  
    class.vsnInputPara                      html  
    computeExprSetPara                      html  
    distributeFiles                         html  
    mergeSplitObjects                       html  
    normalizeAffyBatchConstantPara          html  
    normalizeAffyBatchInvariantsetPara      html  
    normalizeAffyBatchLoessPara             html  
    normalizeAffyBatchLoessParaIter         html  
    normalizeAffyBatchQuantilesPara         html  
    preproPara                              html  
    qa                                      html  
    readAffybatchPara                       html  
    removeDistributedFiles                  html  
    rmaPara                                 html  
    snowReplace                             html  
    split                                   html  
    vsnPara                                 html  
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'affyPara' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affyPara' as affyPara_1.42.0.zip
* DONE (affyPara)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'affyPara' successfully unpacked and MD5 sums checked
In R CMD INSTALL