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Package 82/264HostnameOS / ArchBUILDCHECKBUILD BIN
flowViz 1.3.4
Florian Hahne
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowViz
Last Changed Rev: 30792 / Revision: 30951
Last Changed Date: 2008-04-01 18:50:29 -0700 (Tue, 01 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK [ WARNINGS ]
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: flowViz
Version: 1.3.4
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check flowViz_1.3.4.tar.gz
StartedAt: 2008-04-09 04:10:55 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 04:15:43 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 288.4 seconds
RetCode: 0
Status: WARNINGS
CheckDir: flowViz.Rcheck
Warnings: 5

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/flowViz.Rcheck'
* using R version 2.7.0 beta (2008-04-07 r45159)
* using session charset: ISO8859-1
* checking for file 'flowViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowViz' version '1.3.4'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'flowViz' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:13", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:14", when none found
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 ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:23", when none found
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:26", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:27", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:27", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:27", when none found
See the chapter 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:35", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:36", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:36", when none found
Warning in getPackageName(where) :
  Created a package name, "2008-04-09 04:11:36", when none found
Undocumented code objects:
  glines glpoints glpolygon gpoints gpolygon
Undocumented S4 methods:
  generic 'glines' and siglist 'filter,missing'
  generic 'glines' and siglist 'filterResult,missing'
  generic 'glines' and siglist 'filterResult,flowFrame'
  generic 'glines' and siglist 'rectangleGate,character'
  generic 'glines' and siglist 'rectangleGate,filterResult'
  generic 'glines' and siglist 'rectangleGate,flowFrame'
  generic 'glines' and siglist 'polygonGate,character'
  generic 'glines' and siglist 'polygonGate,filterResult'
  generic 'glines' and siglist 'polygonGate,flowFrame'
  generic 'glines' and siglist 'norm2Filter,ANY'
  generic 'glines' and siglist 'norm2Filter,logicalFilterResult'
  generic 'glines' and siglist 'norm2Filter,flowFrame'
  generic 'glines' and siglist 'curv2Filter,ANY'
  generic 'glines' and siglist 'curv2Filter,multipleFilterResult'
  generic 'glines' and siglist 'curv2Filter,flowFrame'
  generic 'glines' and siglist 'curv1Filter,ANY'
  generic 'glines' and siglist 'curv1Filter,multipleFilterResult'
  generic 'glines' and siglist 'curv1Filter,flowFrame'
  generic 'glines' and siglist 'kmeansFilter,ANY'
  generic 'glpoints' and siglist 'filter,flowFrame,missing'
  generic 'glpoints' and siglist 'filterResult,flowFrame,character'
  generic 'glpoints' and siglist 'rectangleGate,flowFrame,character'
  generic 'glpoints' and siglist 'polygonGate,flowFrame,character'
  generic 'glpoints' and siglist 'norm2Filter,flowFrame,character'
  generic 'glpoints' and siglist 'curv2Filter,flowFrame,character'
  generic 'glpoints' and siglist 'curv1Filter,flowFrame,character'
  generic 'glpoints' and siglist 'kmeansFilter,flowFrame,character'
  generic 'glpolygon' and siglist 'filter,missing'
  generic 'glpolygon' and siglist 'filterResult,missing'
  generic 'glpolygon' and siglist 'filterResult,flowFrame'
  generic 'glpolygon' and siglist 'rectangleGate,character'
  generic 'glpolygon' and siglist 'rectangleGate,filterResult'
  generic 'glpolygon' and siglist 'rectangleGate,flowFrame'
  generic 'glpolygon' and siglist 'polygonGate,character'
  generic 'glpolygon' and siglist 'polygonGate,filterResult'
  generic 'glpolygon' and siglist 'polygonGate,flowFrame'
  generic 'glpolygon' and siglist 'norm2Filter,ANY'
  generic 'glpolygon' and siglist 'norm2Filter,logicalFilterResult'
  generic 'glpolygon' and siglist 'norm2Filter,flowFrame'
  generic 'glpolygon' and siglist 'curv2Filter,ANY'
  generic 'glpolygon' and siglist 'curv2Filter,multipleFilterResult'
  generic 'glpolygon' and siglist 'curv2Filter,flowFrame'
  generic 'glpolygon' and siglist 'curv1Filter,ANY'
  generic 'glpolygon' and siglist 'curv1Filter,multipleFilterResult'
  generic 'glpolygon' and siglist 'curv1Filter,flowFrame'
  generic 'glpolygon' and siglist 'kmeansFilter,ANY'
  generic 'gpoints' and siglist 'filter,flowFrame,missing'
  generic 'gpoints' and siglist 'filterResult,flowFrame,character'
  generic 'gpoints' and siglist 'rectangleGate,flowFrame,character'
  generic 'gpoints' and siglist 'polygonGate,flowFrame,character'
  generic 'gpoints' and siglist 'norm2Filter,flowFrame,character'
  generic 'gpoints' and siglist 'curv2Filter,flowFrame,character'
  generic 'gpoints' and siglist 'curv1Filter,flowFrame,character'
  generic 'gpoints' and siglist 'kmeansFilter,flowFrame,character'
  generic 'gpolygon' and siglist 'filter,missing'
  generic 'gpolygon' and siglist 'filterResult,missing'
  generic 'gpolygon' and siglist 'filterResult,flowFrame'
  generic 'gpolygon' and siglist 'rectangleGate,character'
  generic 'gpolygon' and siglist 'rectangleGate,filterResult'
  generic 'gpolygon' and siglist 'rectangleGate,flowFrame'
  generic 'gpolygon' and siglist 'polygonGate,character'
  generic 'gpolygon' and siglist 'polygonGate,filterResult'
  generic 'gpolygon' and siglist 'polygonGate,flowFrame'
  generic 'gpolygon' and siglist 'norm2Filter,ANY'
  generic 'gpolygon' and siglist 'norm2Filter,logicalFilterResult'
  generic 'gpolygon' and siglist 'norm2Filter,flowFrame'
  generic 'gpolygon' and siglist 'curv2Filter,ANY'
  generic 'gpolygon' and siglist 'curv2Filter,multipleFilterResult'
  generic 'gpolygon' and siglist 'curv2Filter,flowFrame'
  generic 'gpolygon' and siglist 'curv1Filter,ANY'
  generic 'gpolygon' and siglist 'curv1Filter,multipleFilterResult'
  generic 'gpolygon' and siglist 'curv1Filter,flowFrame'
  generic 'gpolygon' and siglist 'kmeansFilter,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'timeLinePlot':
timeLinePlot
  Code: function(x, channel, type = c("stacked", "scaled", "native"),
                 col, ylab = names(x), binSize, varCut = 1, ...)
  Docs: function(x, channel, type = c("stacked", "scaled", "native"),
                 col, ylab = names(x), ...)
  Argument names in code not in docs:
    binSize varCut
  Mismatches in argument names:
    Position: 6 Code: binSize Docs: ...

Codoc mismatches from documentation object 'xyplot':
panel.xyplot.flowset
  Code: function(x, frames, channel.x, channel.y, channel.x.name,
                 channel.y.name, filter = NULL, filterResults = NULL,
                 pch = ".", smooth = TRUE, ...)
  Docs: function(x, frames, channel.x, channel.y, channel.x.name,
                 channel.y.name, filter = NULL, filterResults = NULL,
                 displayFilter = TRUE, pch, smooth, ...)
  Argument names in docs not in code:
    displayFilter
  Mismatches in argument names:
    Position: 9 Code: pch Docs: displayFilter
    Position: 10 Code: smooth Docs: pch
    Position: 11 Code: ... Docs: smooth
  Mismatches in argument default values:
    Name: pch Code: . Docs: 
    Name: smooth Code: TRUE Docs: 

* checking Rd \usage sections ... OK
* creating flowViz-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating flowViz-manual.tex ... OK
* checking flowViz-manual.tex using pdflatex ... OK

WARNING: There were 5 warnings, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/flowViz.Rcheck/00check.log
for details

flowViz.Rcheck/00install.out:

* Installing *source* package 'flowViz' ...
** R
** inst
** preparing package for lazy loading
Loading required package: flowCore
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: rrcov
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 0.4-05)

Attaching package: 'rrcov'


	The following object(s) are masked from package:stats :

	 biplot,
	 predict,
	 screeplot 

Loading required package: feature
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: misc3d
Loading required package: rgl

Attaching package: 'flowCore'


	The following object(s) are masked from package:Biobase :

	 description 


	The following object(s) are masked from package:stats :

	 filter 

Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
Loading required package: MASS
Loading required package: RColorBrewer
Creating a new generic function for "ecdfplot" in "flowViz"
Creating a new generic function for "densityplot" in "flowViz"
Creating a new generic function for "levelplot" in "flowViz"
Creating a new generic function for "qqmath" in "flowViz"
Creating a new generic function for "splom" in "flowViz"
Creating a new generic function for "parallel" in "flowViz"
Creating a new generic function for "xyplot" in "flowViz"
** help
 >>> Building/Updating help pages for package 'flowViz'
     Formats: text html latex example 
  ecdfplot                          text    html    latex   example
  flowPlot                          text    html    latex   example
  flowViz-package                   text    html    latex   example
  latticeMethods-flowSet            text    html    latex   example
  timeLinePlot                      text    html    latex   example
  xyplot                            text    html    latex   example
** building package indices ...
* DONE (flowViz)