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BioC 2.12: CHECK report for iFlow on petty

This page was generated on 2013-10-09 09:39:49 -0700 (Wed, 09 Oct 2013).

Package 336/671HostnameOS / ArchBUILDCHECKBUILD BIN
iFlow 2.12.0
Kyongryun Lee
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/iFlow
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: iFlow
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iFlow_2.12.0.tar.gz
StartedAt: 2013-10-08 22:49:20 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:55:20 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 360.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: iFlow.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/iFlow.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'iFlow/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iFlow' version '2.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'iFlow' can be installed ... [34s/35s] OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
* 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 ... OK
* checking R code for possible problems ... NOTE
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

cleanupEnv: warning in ls(guiEnv(), all = TRUE): partial argument match
  of 'all' to 'all.names'
gpaset.func: warning in normalization(normFun = function(x, parameters,
  ...) gpaSet(x, parameters, ...), parameters = channels[inds],
  arguments = list(bgChannels = channels[bg], register =
  "backgating")): partial argument match of 'normFun' to 'normFunction'
normal.menu: warning in normalization(normFun = function(x, parameters,
  ...) warpSet(x, parameters, ...), parameters = channels[inds],
  arguments = list(grouping = NULL)): partial argument match of
  'normFun' to 'normFunction'
normal.menu: warning in normalization(normFun = function(x, parameters,
  ...) gaussNorm(x, parameters, ...), parameters = channels[inds],
  arguments = list(grouping = NULL)): partial argument match of
  'normFun' to 'normFunction'
ask.dialog: no visible binding for global variable 'selected.channels'
ask.graphics.details: no visible binding for global variable
  'selected.channels'
openGraphics: no visible binding for global variable 'value.y'
openGraphics: no visible binding for global variable 'value.x'
* 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 examples ... [20s/22s] WARNING
Found the following significant warnings:

  Warning: 'method' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/iFlow.Rcheck/00check.log'
for details.

iFlow.Rcheck/00install.out:

* installing *source* package 'iFlow' ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
* DONE (iFlow)

iFlow.Rcheck/iFlow-Ex.timings:

nameusersystemelapsed
GlobalLists0.4440.0070.454
activeFlowset0.4360.0050.441
activeNodeID0.0090.0050.014
activeNodeName0.0070.0030.011
activeWorkflow0.0090.0040.013
getNewName0.0070.0040.011
guiEnv0.0090.0050.015
iflow0.9410.1272.054
isAnyActive0.4450.0040.450
show.message0.0080.0040.011