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 2.13: CHECK report for PREDA on moscato1

This page was generated on 2014-04-05 09:50:26 -0700 (Sat, 05 Apr 2014).

Package 543/750HostnameOS / ArchBUILDCHECKBUILD BIN
PREDA 1.8.0
Francesco Ferrari
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/PREDA
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: PREDA
Version: 1.8.0
Command: rm -rf PREDA.buildbin-libdir && mkdir PREDA.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PREDA.buildbin-libdir PREDA_1.8.0.tar.gz >PREDA-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=PREDA.buildbin-libdir --install="check:PREDA-install.out" --force-multiarch --no-vignettes --timings PREDA_1.8.0.tar.gz && mv PREDA.buildbin-libdir/* PREDA.Rcheck/ && rmdir PREDA.buildbin-libdir
StartedAt: 2014-04-05 05:56:49 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:59:29 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 160.5 seconds
RetCode: 0
Status:  OK  
CheckDir: PREDA.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/PREDA.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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
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 whether package 'PREDA' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'Biobase' 'annotate' '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 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 ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [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

NOTE: There were 6 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/PREDA.Rcheck/00check.log'
for details.

PREDA.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'PREDA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PREDA' as PREDA_1.8.0.zip
* DONE (PREDA)

PREDA.Rcheck/examples_i386/PREDA-Ex.timings:

nameusersystemelapsed
DataForPREDA-class000
GenomicAnnotations-class000
GenomicAnnotations2GenomicAnnotationsForPREDA0.000.010.01
GenomicAnnotationsForPREDA-class000
GenomicAnnotationsForPREDAFromfile0.020.000.02
GenomicAnnotationsFromLibrary0.010.000.01
GenomicAnnotationsFromfile000
GenomicRegions-class0.020.000.02
GenomicRegions2dataframe000
GenomicRegionsFindOverlap000
PREDADataAndResults-class0.020.000.01
PREDAResults-class000
PREDAResults2GenomicRegions0.010.000.02
PREDA_main000
SODEGIRpreprocessingGE0.020.000.01
StatisticsForPREDA-class000
StatisticsForPREDAFromdataframe0.000.020.02
StatisticsForPREDAFromfile000
analysesNames1.350.032.17
computeDatasetSignature000
eset2GenomicAnnotations0.010.000.01
genomePlot000
preprocessingGE0.020.000.02
statisticsForPREDAfromEset000

PREDA.Rcheck/examples_x64/PREDA-Ex.timings:

nameusersystemelapsed
DataForPREDA-class0.010.000.01
GenomicAnnotations-class000
GenomicAnnotations2GenomicAnnotationsForPREDA000
GenomicAnnotationsForPREDA-class0.010.000.01
GenomicAnnotationsForPREDAFromfile000
GenomicAnnotationsFromLibrary000
GenomicAnnotationsFromfile0.000.010.01
GenomicRegions-class000
GenomicRegions2dataframe0.020.000.02
GenomicRegionsFindOverlap000
PREDADataAndResults-class000
PREDAResults-class0.000.010.01
PREDAResults2GenomicRegions000
PREDA_main000
SODEGIRpreprocessingGE000
StatisticsForPREDA-class000
StatisticsForPREDAFromdataframe000
StatisticsForPREDAFromfile000
analysesNames1.350.051.40
computeDatasetSignature000
eset2GenomicAnnotations000
genomePlot000
preprocessingGE000
statisticsForPREDAfromEset000