Package: iFlow

Version: 2.9.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch iFlow_2.9.0.tar.gz

StartedAt: 2012-06-21 01:01:57 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 01:06:25 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 267.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: iFlow.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/iFlow.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'iFlow/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'iFlow' version '2.9.0'
* 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 whether package 'iFlow' can be installed ... 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 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
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 ... 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 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/iFlow.Rcheck/00check.log'
for details.

* installing *source* package 'iFlow' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'iflow.Rnw' 
** testing if installed package can be loaded

* DONE (iFlow)

name	user	system	elapsed
GlobalLists	0.012	0.000	0.013
activeFlowset	0.001	0.000	0.001
activeNodeID	0.000	0.000	0.001
activeNodeName	0.000	0.000	0.001
activeWorkflow	0	0	0
getNewName	0.000	0.000	0.001
guiEnv	0.001	0.001	0.001
iflow	0.935	0.070	1.323
isAnyActive	0	0	0
show.message	0.000	0.001	0.000