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Package 486/658HostnameOS / ArchBUILDCHECKBUILD BIN
PREDA 1.5.0
Francesco Ferrari
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/PREDA
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: PREDA
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PREDA_1.5.0.tar.gz
StartedAt: 2013-03-25 04:07:49 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:10:24 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 155.1 seconds
RetCode: 0
Status:  OK 
CheckDir: PREDA.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/PREDA.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.5.0'
* 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 ... [14s/15s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call with 'PACKAGE' argument in 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 examples ... [10s/10s] 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

NOTE: There were 4 notes.
See
  '/Users/biocbuild/bbs-2.12-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
   'PREDAclasses.Rnw' using 'latin1' 
   'PREDAtutorial.Rnw' using 'latin1' 
** testing if installed package can be loaded
* DONE (PREDA)

PREDA.Rcheck/PREDA-Ex.timings:

nameusersystemelapsed
DataForPREDA-class0.0100.0070.017
GenomicAnnotations-class0.0060.0060.012
GenomicAnnotations2GenomicAnnotationsForPREDA0.0120.0100.025
GenomicAnnotationsForPREDA-class0.0100.0070.016
GenomicAnnotationsForPREDAFromfile0.0180.0160.034
GenomicAnnotationsFromLibrary0.0090.0090.018
GenomicAnnotationsFromfile0.0150.0140.030
GenomicRegions-class0.0060.0070.012
GenomicRegions2dataframe0.0130.0120.025
GenomicRegionsFindOverlap0.0130.0120.025
PREDADataAndResults-class0.0070.0060.015
PREDAResults-class0.0090.0070.016
PREDAResults2GenomicRegions0.0090.0090.018
PREDA_main0.0050.0040.009
SODEGIRpreprocessingGE0.0160.0170.041
StatisticsForPREDA-class0.0060.0060.013
StatisticsForPREDAFromdataframe0.0120.0110.025
StatisticsForPREDAFromfile0.0120.0120.024
analysesNames1.4670.1541.625
computeDatasetSignature0.0130.0120.026
eset2GenomicAnnotations0.0080.0080.017
genomePlot0.0070.0060.013
preprocessingGE0.0150.0140.033
statisticsForPREDAfromEset0.0130.0100.024