affyPara 1.33.0
Markus Schmidberger
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affyPara | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/affyPara.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affyPara/DESCRIPTION’ ... OK
* this is package ‘affyPara’ version ‘1.33.0’
* 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 ‘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
* 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 loading without being on the library search path ... 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 sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘vsnStudy.pdf’ from 2114Kb to 316Kb
consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 5 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/affyPara.Rcheck/00check.log’
for details.