BioC 2.13: CHECK report for PREDA on perceval

Package: PREDA

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PREDA_1.8.0.tar.gz

StartedAt: 2014-04-05 03:29:24 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 03:32:14 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 169.8 seconds

RetCode: 0

Status:  OK

CheckDir: PREDA.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/PREDA.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘Rmpi’ ‘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 ... [16s/16s] 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.
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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 the chapter ‘System and foreign language interfaces’ of 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'
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’
* 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’ ... NOTE
The following directories should probably not be installed:
  ‘images’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘PREDAclasses.Rnw’, ‘PREDAtutorial.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [11s/11s] 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

NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/PREDA.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
DataForPREDA-class	0.010	0.002	0.012
GenomicAnnotations-class	0.007	0.001	0.008
GenomicAnnotations2GenomicAnnotationsForPREDA	0.007	0.001	0.008
GenomicAnnotationsForPREDA-class	0.008	0.001	0.010
GenomicAnnotationsForPREDAFromfile	0.016	0.001	0.018
GenomicAnnotationsFromLibrary	0.009	0.001	0.009
GenomicAnnotationsFromfile	0.013	0.002	0.015
GenomicRegions-class	0.009	0.001	0.011
GenomicRegions2dataframe	0.012	0.001	0.014
GenomicRegionsFindOverlap	0.017	0.002	0.019
PREDADataAndResults-class	0.011	0.002	0.013
PREDAResults-class	0.010	0.001	0.012
PREDAResults2GenomicRegions	0.009	0.002	0.012
PREDA_main	0.008	0.001	0.009
SODEGIRpreprocessingGE	0.021	0.001	0.025
StatisticsForPREDA-class	0.006	0.000	0.007
StatisticsForPREDAFromdataframe	0.012	0.001	0.014
StatisticsForPREDAFromfile	0.015	0.001	0.016
analysesNames	2.459	0.089	2.600
computeDatasetSignature	0.014	0.010	0.024
eset2GenomicAnnotations	0.024	0.006	0.030
genomePlot	0.002	0.001	0.004
preprocessingGE	0.015	0.007	0.021
statisticsForPREDAfromEset	0.008	0.004	0.013