Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.4: CHECK report for affyPara on zin1

This page was generated on 2016-09-21 03:36:31 -0700 (Wed, 21 Sep 2016).

Package 25/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affyPara
Version: 1.33.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.33.0.tar.gz
StartedAt: 2016-09-20 02:59:58 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 03:00:49 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 50.3 seconds
RetCode: 0
Status:  OK 
CheckDir: affyPara.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings affyPara_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* 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.


affyPara.Rcheck/00install.out:

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

affyPara.Rcheck/affyPara-Ex.timings:

nameusersystemelapsed
MAplotPara0.0040.0000.001
bgcPara000
boxplotPara0.0040.0000.001
computeExprSetPara0.0000.0000.001
distributeFiles000
mergeSplitObjects0.9880.0121.000
normalizeAffyBatchConstantPara000
normalizeAffyBatchInvariantsetPara000
normalizeAffyBatchLoessPara0.0000.0000.001
normalizeAffyBatchLoessParaIter0.0040.0000.000
normalizeAffyBatchQuantilesPara0.0000.0000.001
preproPara0.0000.0000.001
qa0.0000.0000.001
readAffybatchPara0.0000.0000.001
removeDistributedFiles0.0040.0000.000
rmaPara0.0000.0000.001
snowReplace0.0000.0000.001
split0.3920.0120.403
vsnPara0.0000.0000.001