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Package 195/251HostnameOS / ArchBUILDCHECKBUILD BIN
rflowcyt 1.11.0
N. LeMeur
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rflowcyt
Last Changed Rev: 27847 / Revision: 29143
Last Changed Date: 2007-10-08 11:45:32 -0700 (Mon, 08 Oct 2007)
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 
lemming Windows Server 2003 (32-bit) / x64  OK  WARNINGS  OK 
Package: rflowcyt
Version: 1.11.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check rflowcyt_1.11.0.tar.gz
StartedAt: 2007-12-11 08:15:47 -0800 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 08:35:44 -0800 (Tue, 11 Dec 2007)
EllapsedTime: 1197.2 seconds
RetCode: 0
Status: WARNINGS
CheckDir: rflowcyt.Rcheck
Warnings: 2

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-09 r43632)
* checking for file 'rflowcyt/DESCRIPTION' ... OK
* this is package 'rflowcyt' version '1.11.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rflowcyt' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
Rd files without 'description':
  FCSggobi-class.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[<-' and siglist 'FCS,ANY,ANY'
  generic '[<-' and siglist 'FCSmetadata,ANY,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 ... OK
* checking Rd \usage sections ... OK
* creating rflowcyt-Ex.R ... OK
* checking examples ... OK
* checking tests ...
make[1]: Entering directory `/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck/tests'
  Running 'FCSclass-tests.R'
  Running 'FCSgateclass-tests.R'
  Running 'FCSmetadataclass-tests.R'
  Running 'fluors.FCS.R'
  Running 'read.FCS-tests.R'
  Running 'runflowcytests-tests.R'
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rflowcyt.tex' ...
Package natbib Warning: Citation `robin:2001' on page 2 undefined on input line
Package natbib Warning: Citation `robin:2001' on page 3 undefined on input line
Package natbib Warning: Citation `gasparetto:smith:2004' on page 15 undefined o
Package natbib Warning: Citation `gasparetto:smith:2004' on page 22 undefined o
Package natbib Warning: Citation `roe:hardy:2001' on page 34 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 41 undefined on input
Package natbib Warning: Citation `fried:fish:1998' on page 42 undefined on inpu
Package natbib Warning: Citation `roe:hardy:2001' on page 43 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 43 undefined on input
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 48 undefined 
Package natbib Warning: Citation `baggerly:2001' on page 48 undefined on input 
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 52 undefined 
Package natbib Warning: Citation `baggerly:2001' on page 52 undefined on input 
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rflowcyt.tex' ...
Package natbib Warning: Citation `robin:2001' on page 3 undefined on input line
Package natbib Warning: Citation `robin:2001' on page 4 undefined on input line
Package natbib Warning: Citation `gasparetto:smith:2004' on page 16 undefined o
Package natbib Warning: Citation `gasparetto:smith:2004' on page 23 undefined o
Package natbib Warning: Citation `roe:hardy:2001' on page 35 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 42 undefined on input
Package natbib Warning: Citation `fried:fish:1998' on page 43 undefined on inpu
Package natbib Warning: Citation `roe:hardy:2001' on page 44 undefined on input
Package natbib Warning: Citation `roe:hardy:2001' on page 44 undefined on input
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 49 undefined 
Package natbib Warning: Citation `baggerly:2001' on page 49 undefined on input 
Package natbib Warning: Citation `roe:tre:moore:her:2001' on page 53 undefined 
Package natbib Warning: Citation `baggerly:2001' on page 53 undefined on input 
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './rflowcyt.tex' ...
* creating rflowcyt-manual.tex ... OK
* checking rflowcyt-manual.tex ... OK

WARNING: There were 2 warnings, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck/00check.log
for details

rflowcyt.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/rflowcyt.Rcheck
* Installing *source* package 'rflowcyt' ...
** R
** inst
** preparing package for lazy loading
Loading required package: survival
Loading required package: splines
Loading required package: xtable
Loading required package: KernSmooth
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: MASS
Loading required package: grid
Loading required package: hexbin
Loading required package: lattice
Loading required package: rfcdmin
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded.  Version 0.13-1 (2007-12-03).

Type demo( spam) for some demos, help( Spam) for an overview of this library.


Attaching package: 'spam'


	The following object(s) are masked _by_ .GlobalEnv :

	 .Spam 


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

	 display 

 Try help(fields) for an overview of this library 
Loading required package: locfit
Loading required package: akima
locfit 1.5-4 	 2007-11-27 
Loading required package: splancs
Loading required package: sp

Spatial Point Pattern Analysis Code in S-Plus

 Version 2 - Spatial and Space-Time analysis
Loading required package: prada
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: RColorBrewer
Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'


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

	 heart 

Scalable Robust Estimators with High Breakdown Point (version 0.4-03)

Attaching package: 'rrcov'


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

	 biplot,
	 predict,
	 screeplot 

Loading required package: xgobi
** help
Note: removing empty section \description
Note: removing empty section \examples
Note: removing empty section \value
 >>> Building/Updating help pages for package 'rflowcyt'
     Formats: text html latex example 
  ContourScatterPlot                text    html    latex   example
  FCS-class                         text    html    latex   example
  FCSgate-class                     text    html    latex   example
  FCSggobi-class                    text    html    latex
  FCSmetadata-class                 text    html    latex   example
  FCSsummary-class                  text    html    latex   example
  FHCRC.HVTNFCS                     text    html    latex   example
  ImageParCoord                     text    html    latex   example
  KS.flowcytest                     text    html    latex   example
  MODE                              text    html    latex   example
  PercentPos.FCS                    text    html    latex   example
  ProbBin.FCS                       text    html    latex   example
  ProbBin.flowcytest                text    html    latex   example
  ROC.FCS                           text    html    latex   example
  VRC.HVTNFCS                       text    html    latex   example
  WLR.flowcytest                    text    html    latex   example
  add.parallel.coordinates          text    html    latex   example
  add.parallelCoordinates           text    html    latex   example
  addParameter-methods              text    html    latex
  boxplot.FCS                       text    html    latex   example
  breakpoints.ProbBin               text    html    latex   example
  checkvars-methods                 text    html    latex
  coerce-FCSformat                  text    html    latex   example
  coerce-methods                    text    html    latex
  convertS3toS4                     text    html    latex   example
  createGate                        text    html    latex   example
  cytoSet-class                     text    html    latex   example
  dim.FCS-methods                   text    html    latex
  emp.f                             text    html    latex   example
  equals-methods                    text    html    latex
  extractGateHistory                text    html    latex   example
  extractGatedData                  text    html    latex   example
  fcs.type                          text    html    latex   example
  fixvars-methods                   text    html    latex
  fluors-methods                    text    html    latex
  gate.IPC                          text    html    latex   example
  get.h                             text    html    latex   example
  get.num.modes                     text    html    latex   example
  get.p                             text    html    latex   example
  ggobi-methods                     text    html    latex
  legend.CSP                        text    html    latex   example
  make.grid                         text    html    latex   example
  metaData-methods                  text    html    latex
  pairs.CSP                         text    html    latex   example
  parallelCoordinates               text    html    latex   example
  pkci2.flowcytest                  text    html    latex   example
  plot-methods                      text    html    latex
  plot.ProbBin.FCS                  text    html    latex   example
  plot2sets.FCS                     text    html    latex   example
  plotECDF.FCS                      text    html    latex   example
  plotQA.FCS                        text    html    latex   example
  plotdensity.FCS                   text    html    latex   example
  plotvar.FCS                       text    html    latex   example
  print-methods                     text    html    latex
  read.FCS                          text    html    latex   example
  read.series.FCS                   text    html    latex   example
  rect.box.idx                      text    html    latex   example
  rflowcyt-defunct                  text    html    latex
  runflowcytests                    text    html    latex   example
  show-methods                      text    html    latex
  showgate.FCS                      text    html    latex   example
  standard                          text    html    latex   example
  subset-methods                    text    html    latex
  subset2-methods                   text    html    latex
  subset2assign-methods             text    html    latex
  subsetassign-methods              text    html    latex
  summary-methods                   text    html    latex
  summary.ProbBin.FCS               text    html    latex   example
  xgobi.FCS                         text    html    latex   example
** building package indices ...
* DONE (rflowcyt)