Package: rflowcyt

Version: 1.25.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings rflowcyt_1.25.0.tar.gz

StartedAt: 2011-04-20 15:39:56 -0700 (Wed, 20 Apr 2011)

EndedAt: 2011-04-20 15:44:42 -0700 (Wed, 20 Apr 2011)

EllapsedTime: 285.6 seconds

RetCode: 0

Status:  OK

CheckDir: rflowcyt.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/rflowcyt.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rflowcyt/DESCRIPTION' ... OK
* this is package 'rflowcyt' version '1.25.0'
* 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 installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking Rd files ... NOTE
prepare_Rd: FCSggobi-class.Rd:27-28: Dropping empty section \examples
prepare_Rd: rect.box.idx.Rd:34-36: Dropping empty section \value
* 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 ... NOTE
'library' or 'require' call not declared from: 'rfcprim'
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking 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'
 OK
* 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

* installing *source* package 'rflowcyt' ...
** R
** inst
** preparing package for lazy loading
Loading required package: spam
Package 'spam' is loaded. Spam version 0.23-0 (2010-09-01).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained by adding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.

Attaching package: 'spam'

The following object(s) are masked from 'package:base':

    backsolve, forwardsolve, norm

 Use help(fields) for an overview of this library

library( fields, keep.source=TRUE) retains comments in the source code. 
Loading required package: grid
Loading required package: lattice
Loading required package: akima
locfit 1.5-6 	 2010-01-20 
Loading required package: Biobase

Welcome to Bioconductor

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

Loading required package: RColorBrewer
Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
Scalable Robust Estimators with High Breakdown Point (version 1.2-01)
Loading required package: sp

Spatial Point Pattern Analysis Code in S-Plus

 Version 2 - Spatial and Space-Time analysis
Loading required package: splines

Attaching package: 'survival'

The following object(s) are masked from 'package:robustbase':

    heart


Attaching package: 'xtable'

The following object(s) are masked from 'package:spam':

    display

KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'rflowcyt.Rnw' 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.2-01)

Spatial Point Pattern Analysis Code in S-Plus

 Version 2 - Spatial and Space-Time analysis

*** Deprecation warning ***:
The package 'rflowcyt' is deprecated and will not be supported after Bioconductor release 2.4. 
    Similar functionality is provided in packages flowCore and flowViz .



* DONE (rflowcyt)

name	user	system	elapsed
ContourScatterPlot	5.06	0.03	5.30
FCS-class	0.06	0.00	0.06
FCSgate-class	0	0	0
FCSmetadata-class	0.00	0.02	0.02
FCSsummary-class	0	0	0
FHCRC.HVTNFCS	0.35	0.00	0.34
ImageParCoord	2.97	0.02	2.99
KS.flowcytest	2.92	0.01	2.93
MODE	0.00	0.00	0.02
PercentPos.FCS	3.34	0.03	3.37
ProbBin.FCS	3.02	0.00	3.02
ProbBin.flowcytest	2.86	0.02	2.87
ROC.FCS	0.01	0.00	0.04
VRC.HVTNFCS	3	0	3
WLR.flowcytest	2.92	0.06	2.99
add.parallel.coordinates	0.33	0.00	0.32
add.parallelCoordinates	0.42	0.02	0.44
boxplot.FCS	7.27	0.11	7.50
breakpoints.ProbBin	0.01	0.00	0.02
coerce-FCSformat	0	0	0
convertS3toS4	0.02	0.00	0.07
createGate	1.72	0.07	1.80
cytoSet-class	0.32	0.00	0.55
emp.f	0.02	0.00	0.01
extractGateHistory	1.44	0.02	1.46
extractGatedData	1.51	0.05	1.56
fcs.type	0.13	0.00	0.12
gate.IPC	2.89	0.00	2.90
get.h	0.04	0.00	0.04
get.num.modes	0.08	0.00	0.08
get.p	1.22	0.00	1.22
legend.CSP	4.39	0.00	4.41
make.grid	11.24	0.34	11.62
pairs.CSP	0	0	0
parallelCoordinates	0.31	0.00	0.31
pkci2.flowcytest	2.84	0.02	2.89
plot.ProbBin.FCS	2.83	0.06	2.89
plot2sets.FCS	0	0	0
plotECDF.FCS	7.67	0.01	7.69
plotQA.FCS	31.85	0.02	31.95
plotdensity.FCS	0.42	0.00	0.43
plotvar.FCS	0	0	0
read.FCS	0.01	0.00	0.01
read.series.FCS	0.1	0.0	0.1
rect.box.idx	0.01	0.02	0.07
runflowcytests	2.89	0.00	2.89
showgate.FCS	0	0	0
standard	0	0	0
summary.ProbBin.FCS	2.85	0.01	2.85
xgobi.FCS	2.78	0.03	2.83