BioC 2.9: CHECK report for PREDA on pitt

Package: PREDA

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PREDA_1.0.0.tar.gz

StartedAt: 2012-03-24 03:21:56 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 03:24:51 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 174.5 seconds

RetCode: 0

Status: OK

CheckDir: PREDA.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/PREDA.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'PREDA/DESCRIPTION' ... OK
* this is package 'PREDA' version '1.0.0'
* 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 whether package 'PREDA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'PREDA' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'PREDAclasses.Rnw' using 'latin1' 
   'PREDAtutorial.Rnw' using 'latin1' 
** testing if installed package can be loaded

* DONE (PREDA)

name	user	system	elapsed
DataForPREDA-class	0.003	0.001	0.003
GenomicAnnotations-class	0.001	0.000	0.001
GenomicAnnotations2GenomicAnnotationsForPREDA	0.000	0.000	0.001
GenomicAnnotationsForPREDA-class	0.001	0.001	0.001
GenomicAnnotationsForPREDAFromfile	0.001	0.000	0.001
GenomicAnnotationsFromLibrary	0.000	0.001	0.000
GenomicAnnotationsFromfile	0	0	0
GenomicRegions-class	0.000	0.001	0.001
GenomicRegions2dataframe	0.001	0.000	0.000
GenomicRegionsFindOverlap	0	0	0
PREDADataAndResults-class	0.001	0.000	0.001
PREDAResults-class	0.001	0.000	0.001
PREDAResults2GenomicRegions	0	0	0
PREDA_main	0.001	0.000	0.000
SODEGIRpreprocessingGE	0	0	0
StatisticsForPREDA-class	0.001	0.000	0.001
StatisticsForPREDAFromdataframe	0	0	0
StatisticsForPREDAFromfile	0	0	0
analysesNames	2.637	0.148	3.585
computeDatasetSignature	0	0	0
eset2GenomicAnnotations	0	0	0
genomePlot	0	0	0
preprocessingGE	0	0	0
statisticsForPREDAfromEset	0.000	0.001	0.001

Summary

Command output