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BioC 3.2: CHECK report for PREDA on perceval

This page was generated on 2015-10-27 17:34:42 -0400 (Tue, 27 Oct 2015).

Package 793/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PREDA 1.16.0
Francesco Ferrari
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/PREDA
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  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PREDA
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PREDA_1.16.0.tar.gz
StartedAt: 2015-10-27 11:04:51 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 11:06:44 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 113.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PREDA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PREDA_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/PREDA.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PREDA/DESCRIPTION’ ... OK
* this is package ‘PREDA’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘rsprng’
* 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 ‘PREDA’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘annotate’ ‘lokern’ ‘multtest’ ‘stats’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘affy’ ‘caTools’ ‘limma’ ‘quantsmooth’ ‘qvalue’ ‘Rmpi’ ‘rsprng’
  ‘samr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘annotate’ ‘Biobase’ ‘lokern’ ‘methods’ ‘multtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("mpi_finalize", ..., PACKAGE = "Rmpi")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
genomePlot_improved: warning in axis(1, seq(from = 0, to = max(len), by
  = (10 * scale.positions)), label = as.integer(((seq(from = 0, to =
  max(len), by = (10 * scale.positions))/scale.positions)))): partial
  argument match of 'label' to 'labels'
genomePlot,GenomicAnnotationsForPREDA : .local: warning in axis(1,
  seq(from = 0, to = max(len), by = (10 * scale.positions)), label =
  as.integer(((seq(from = 0, to = max(len), by = (10 *
  scale.positions))/scale.positions)))): partial argument match of
  'label' to 'labels'
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘lmFit’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘makeContrasts’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘contrasts.fit’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘eBayes’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘topTable’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘samr’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘samr.compute.delta.table’
GE_computeStatistic_onMatrix: no visible global function definition for
  ‘samr.compute.siggenes.table’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘annPkgName’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘keys’
GenomicAnnotationsFromLibrary: no visible global function definition
  for ‘lookUp’
getExpectedSmoothFunction_runmean : PREDA_runmeanStatPerm_fun: no
  visible global function definition for ‘runmean’
getObservedSmoothFunction_runmean : PREDA_runmeanStat_fun: no visible
  global function definition for ‘runmean’
PREDA_main : .Last: no visible global function definition for
  ‘mpi.comm.size’
PREDA_main : .Last: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_main: no visible global function definition for
  ‘mpi.spawn.Rslaves’
PREDA_main: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
PREDA_main: no visible global function definition for ‘mpi.remote.exec’
PREDA_main: no visible global function definition for ‘init.sprng’
PREDA_main: no visible global function definition for ‘mpi.comm.size’
PREDA_main: no visible global function definition for ‘mpi.comm.rank’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.recv.Robj’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.any.tag’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.get.sourcetag’
PREDA_main : Listen_on_slaves: no visible global function definition
  for ‘mpi.send.Robj’
PREDA_main: no visible global function definition for ‘mpi.isend.Robj’
PREDA_main: no visible global function definition for ‘mpi.bcast.cmd’
PREDA_main: no visible global function definition for ‘mpi.recv.Robj’
PREDA_main: no visible global function definition for ‘mpi.any.source’
PREDA_main: no visible global function definition for ‘mpi.any.tag’
PREDA_main: no visible global function definition for
  ‘mpi.get.sourcetag’
PREDA_main: no visible global function definition for ‘free.sprng’
PREDA_main: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.spawn.Rslaves’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.remote.exec’
PREDA_main_permRows: no visible global function definition for
  ‘init.sprng’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.comm.size’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.comm.rank’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.recv.Robj’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.any.tag’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.get.sourcetag’
PREDA_main_permRows : Listen_on_slaves: no visible global function
  definition for ‘mpi.send.Robj’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.isend.Robj’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.bcast.cmd’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.recv.Robj’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.any.source’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.any.tag’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.get.sourcetag’
PREDA_main_permRows: no visible global function definition for
  ‘free.sprng’
PREDA_main_permRows: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.spawn.Rslaves’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.remote.exec’
PREDA_main_permSamples: no visible global function definition for
  ‘init.sprng’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.comm.size’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.comm.rank’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.recv.Robj’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.any.tag’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.get.sourcetag’
PREDA_main_permSamples : Listen_on_slaves: no visible global function
  definition for ‘mpi.send.Robj’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.isend.Robj’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.bcast.cmd’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.recv.Robj’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.any.source’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.any.tag’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.get.sourcetag’
PREDA_main_permSamples: no visible global function definition for
  ‘free.sprng’
PREDA_main_permSamples: no visible global function definition for
  ‘mpi.close.Rslaves’
PREDA_multTestCorrection: no visible global function definition for
  ‘qvalue’
PREDA_multTestCorrection: no visible global function definition for
  ‘mt.rawp2adjp’
PREDA_quantsmoothStat: no visible global function definition for
  ‘quantsmooth’
PREDA_quantsmoothStatPerm: no visible global function definition for
  ‘quantsmooth’
PREDA_smoothStat: no visible global function definition for ‘lokerns’
PREDA_smoothStatPerm: no visible global function definition for
  ‘lokerns’
RMAwithCDFfilter: no visible global function definition for
  ‘cleancdfname’
RMAwithCDFfilter: no visible global function definition for
  ‘multiassign’
RMAwithCDFfilter: no visible global function definition for
  ‘annotation<-’
RMAwithCDFfilter: no visible global function definition for ‘pData’
RMAwithCDFfilter: no visible global function definition for
  ‘sampleNames’
RMAwithCDFfilter: no visible global function definition for
  ‘phenoData<-’
RMAwithCDFfilter: no visible global function definition for ‘rma’
RMAwithCDFfilter: no visible global function definition for ‘justRMA’
eset2GenomicAnnotations,ExpressionSet : .local: no visible global
  function definition for ‘featureNames’
eset2GenomicAnnotations,ExpressionSet : .local: no visible global
  function definition for ‘annotation’
GE_computeStatistic,ExpressionSet : .local: no visible global function
  definition for ‘pData’
GE_computeStatistic,ExpressionSet : .local: no visible global function
  definition for ‘sampleNames’
GE_computeStatistic,ExpressionSet : .local: no visible global function
  definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet : .local: no visible
  global function definition for ‘pData’
GE_simulations_samplingColumns,ExpressionSet : .local: no visible
  global function definition for ‘exprs’
GE_simulations_samplingColumns,ExpressionSet : .local: no visible
  global function definition for ‘exprs<-’
GE_standardize,ExpressionSet : .local: no visible global function
  definition for ‘exprs’
GE_standardize,ExpressionSet : .local: no visible global function
  definition for ‘exprs<-’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
  definition for ‘pData’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
  definition for ‘exprs’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
  definition for ‘samr’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
  definition for ‘sampleNames’
SODEGIR_GEstatistics,ExpressionSet : .local: no visible global function
  definition for ‘featureNames’
statisticsForPREDAfromEset,ExpressionSet : .local: no visible global
  function definition for ‘pData’
statisticsForPREDAfromEset,ExpressionSet : .local: no visible global
  function definition for ‘sampleNames’
statisticsForPREDAfromEset,ExpressionSet : .local: no visible global
  function definition for ‘featureNames’
* 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’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/PREDA.Rcheck/00check.log’
for details.

PREDA.Rcheck/00install.out:

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

PREDA.Rcheck/PREDA-Ex.timings:

nameusersystemelapsed
DataForPREDA-class0.0030.0010.004
GenomicAnnotations-class0.0020.0000.002
GenomicAnnotations2GenomicAnnotationsForPREDA0.0010.0010.001
GenomicAnnotationsForPREDA-class0.0030.0000.003
GenomicAnnotationsForPREDAFromfile0.0020.0010.003
GenomicAnnotationsFromLibrary0.0000.0000.001
GenomicAnnotationsFromfile0.0010.0010.002
GenomicRegions-class0.0020.0000.003
GenomicRegions2dataframe0.0010.0010.001
GenomicRegionsFindOverlap0.0010.0000.001
PREDADataAndResults-class0.0030.0010.004
PREDAResults-class0.0020.0000.003
PREDAResults2GenomicRegions0.0010.0000.001
PREDA_main0.0000.0000.001
SODEGIRpreprocessingGE0.0010.0010.002
StatisticsForPREDA-class0.0020.0000.001
StatisticsForPREDAFromdataframe0.0010.0000.001
StatisticsForPREDAFromfile0.0000.0000.002
analysesNames1.4500.0471.702
computeDatasetSignature0.0010.0000.002
eset2GenomicAnnotations0.0010.0000.001
genomePlot0.0000.0000.001
preprocessingGE0.0010.0000.001
statisticsForPREDAfromEset0.0010.0000.001