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rflowcyt

1.8.0

N. LeMeur
Last Changed Date: 2007-04-24 11:21:48 -0700
Last Changed Rev: 24214
lamb1 Linux (SUSE 10.1) x86_64  OK  WARNINGS 
wellington Linux (SUSE 9.2) i686  OK  WARNINGS 
lemming Windows Server 2003 (32-bit) x64  OK [ WARNINGS ] OK 
Package: rflowcyt
Version: 1.8.0
Command: D:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check rflowcyt_1.8.0.tar.gz
RetCode: 0
Time: 726.4 seconds
Status: WARNINGS
CheckDir: rflowcyt.Rcheck
Warnings: 3

Command output

* checking for working latex ... OK
* using log directory 'D:/biocbld/bbs-2.0-bioc/meat/rflowcyt.Rcheck'
* using R version 2.5.1 (2007-06-27)
* checking for file 'rflowcyt/DESCRIPTION' ... OK
* this is package 'rflowcyt' version '1.8.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'rflowcyt' can be installed ... WARNING
Found the following significant warnings:
       missing link(s):  xyplot
       missing link(s):  xyplot xyplot xyplot lattice lattice xyplot
See 'D:/biocbld/bbs-2.0-bioc/meat/rflowcyt.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... 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 ... WARNING
parallel:
  function(x, data, ...)
parallel.coordinates:
  function(x, varlabpos, variable.names, my.ylab, my.ylim, at.y,
           each.ylab, scaled, group, group.lty, group.col, group.lwd,
           superimpose)

See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* 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'
  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 `/cygdrive/d/biocbld/bbs-2.0-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 `/cygdrive/d/biocbld/bbs-2.0-bioc/meat/rflowcyt.Rcheck/tests'
 OK
* checking package vignettes in 'inst/doc' ... OK
* creating rflowcyt-manual.tex ... OK
* checking rflowcyt-manual.tex ... OK

WARNING: There were 3 warnings, see
  D:/biocbld/bbs-2.0-bioc/meat/rflowcyt.Rcheck/00check.log
for details

rflowcyt.Rcheck/00install.out:

installing R.css in D:/biocbld/bbs-2.0-bioc/meat/rflowcyt.Rcheck


---------- Making package rflowcyt ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'rflowcyt'
     Formats: text html latex example chm 
  ContourScatterPlot                text    html    latex   example chm
  FCS-class                         text    html    latex   example chm
  FCSgate-class                     text    html    latex   example chm
  FCSggobi-class                    text    html    latex   example chm
  FCSmetadata-class                 text    html    latex   example chm
  FCSsummary-class                  text    html    latex   example chm
  FHCRC.HVTNFCS                     text    html    latex   example chm
  ImageParCoord                     text    html    latex   example chm
  KS.flowcytest                     text    html    latex   example chm
  MODE                              text    html    latex   example chm
  PercentPos.FCS                    text    html    latex   example chm
  ProbBin.FCS                       text    html    latex   example chm
  ProbBin.flowcytest                text    html    latex   example chm
  ROC.FCS                           text    html    latex   example chm
  VRC.HVTNFCS                       text    html    latex   example chm
  WLR.flowcytest                    text    html    latex   example chm
  add.parallel.coordinates          text    html    latex   example chm
  add.parallelCoordinates           text    html    latex   example chm
  addParameter-methods              text    html    latex           chm
  boxplot.FCS                       text    html    latex   example chm
     missing link(s):  xyplot
  breakpoints.ProbBin               text    html    latex   example chm
  checkvars-methods                 text    html    latex           chm
  coerce-FCSformat                  text    html    latex   example chm
  coerce-methods                    text    html    latex           chm
  convertS3toS4                     text    html    latex   example chm
  createGate                        text    html    latex   example chm
  cytoSet-class                     text    html    latex   example chm
  dim.FCS-methods                   text    html    latex           chm
  emp.f                             text    html    latex   example chm
  equals-methods                    text    html    latex           chm
  extractGateHistory                text    html    latex   example chm
  extractGatedData                  text    html    latex   example chm
  fcs.type                          text    html    latex   example chm
  fixvars-methods                   text    html    latex           chm
  fluors-methods                    text    html    latex           chm
  gate.IPC                          text    html    latex   example chm
  get.h                             text    html    latex   example chm
  get.num.modes                     text    html    latex   example chm
  get.p                             text    html    latex   example chm
  ggobi-methods                     text    html    latex           chm
  legend.CSP                        text    html    latex   example chm
  make.grid                         text    html    latex   example chm
  metaData-methods                  text    html    latex           chm
  pairs.CSP                         text    html    latex   example chm
  parallel.coordinates              text    html    latex   example chm
  parallelCoordinates               text    html    latex   example chm
  pkci2.flowcytest                  text    html    latex   example chm
  plot-methods                      text    html    latex           chm
  plot.ProbBin.FCS                  text    html    latex   example chm
  plot2sets.FCS                     text    html    latex   example chm
  plotECDF.FCS                      text    html    latex   example chm
     missing link(s):  xyplot xyplot xyplot lattice lattice xyplot
  plotQA.FCS                        text    html    latex   example chm
  plotdensity.FCS                   text    html    latex   example chm
  plotvar.FCS                       text    html    latex   example chm
  print-methods                     text    html    latex           chm
  read.FCS                          text    html    latex   example chm
  read.series.FCS                   text    html    latex   example chm
  rect.box.idx                      text    html    latex   example chm
  rflowcyt-defunct                  text    html    latex           chm
  runflowcytests                    text    html    latex   example chm
  show-methods                      text    html    latex           chm
  showgate.FCS                      text    html    latex   example chm
  standard                          text    html    latex   example chm
  subset-methods                    text    html    latex           chm
  subset2-methods                   text    html    latex           chm
  subset2assign-methods             text    html    latex           chm
  subsetassign-methods              text    html    latex           chm
  summary-methods                   text    html    latex           chm
  summary.ProbBin.FCS               text    html    latex   example chm
  xgobi.FCS                         text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\bbs-2.0-bioc\meat\rflowcyt.Rcheck\00_pkg_src\rflowcyt\chm\rflowcyt.chm


Compile time: 0 minutes, 0 seconds
71	Topics
560	Local links
1	Internet link
1	Graphic


Created d:\biocbld\bbs-2.0-bioc\meat\rflowcyt.Rcheck\00_pkg_src\rflowcyt\chm\rflowcyt.chm, 176,759 bytes
Compression decreased file by 291,049 bytes.
  preparing package rflowcyt 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: locfit
Loading required package: akima
Loading required package: splancs
Loading required package: sp
Creating a new generic function for "print" in "rflowcyt"
  adding MD5 sums

* DONE (rflowcyt)