Package: rflowcyt

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rflowcyt_1.24.0.tar.gz

StartedAt: 2011-10-20 16:54:58 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:02:00 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 421.6 seconds

RetCode: 0

Status:  OK

CheckDir: rflowcyt.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/rflowcyt.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'rflowcyt/DESCRIPTION' ... OK
* this is package 'rflowcyt' version '1.24.0'
* checking package namespace 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 12.5Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
* 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 ... 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 sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'rflowcyt.pdf' from 11.8Mb to 2.2Mb
  consider running tools::compactPDF() on these files
* 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
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

*** 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	5.916	0.220	6.210
FCS-class	0.094	0.011	0.106
FCSgate-class	0.001	0.000	0.001
FCSmetadata-class	0.021	0.004	0.025
FCSsummary-class	0.001	0.001	0.001
FHCRC.HVTNFCS	0.376	0.013	0.391
ImageParCoord	3.805	0.139	3.947
KS.flowcytest	3.762	0.140	3.911
MODE	0.016	0.001	0.016
PercentPos.FCS	4.431	0.174	4.615
ProbBin.FCS	3.820	0.140	3.976
ProbBin.flowcytest	3.753	0.133	3.898
ROC.FCS	0.007	0.002	0.034
VRC.HVTNFCS	3.832	0.135	3.978
WLR.flowcytest	3.811	0.139	4.058
add.parallel.coordinates	0.364	0.010	0.618
add.parallelCoordinates	0.379	0.011	0.518
boxplot.FCS	8.663	0.520	13.142
breakpoints.ProbBin	0.006	0.000	0.007
coerce-FCSformat	0.002	0.000	0.002
convertS3toS4	0.020	0.007	0.046
createGate	2.382	0.772	5.003
cytoSet-class	0.246	0.041	0.584
emp.f	0.007	0.000	0.012
extractGateHistory	2.032	0.592	3.968
extractGatedData	2.049	0.584	4.111
fcs.type	0.017	0.006	0.029
gate.IPC	3.831	0.134	5.531
get.h	0.050	0.002	0.063
get.num.modes	0.095	0.005	0.129
get.p	1.554	0.009	2.376
legend.CSP	4.960	0.243	7.309
make.grid	11.744	1.388	17.820
pairs.CSP	0.004	0.000	0.005
parallelCoordinates	0.368	0.011	0.380
pkci2.flowcytest	3.685	0.139	3.878
plot.ProbBin.FCS	3.720	0.145	3.984
plot2sets.FCS	0	0	0
plotECDF.FCS	10.481	0.663	11.329
plotQA.FCS	34.776	1.246	36.185
plotdensity.FCS	0.421	0.034	0.456
plotvar.FCS	0.003	0.004	0.008
read.FCS	0.034	0.014	0.049
read.series.FCS	0.088	0.016	0.105
rect.box.idx	0.016	0.003	0.048
runflowcytests	3.728	0.155	3.887
showgate.FCS	0.002	0.000	0.003
standard	0.002	0.000	0.002
summary.ProbBin.FCS	3.731	0.151	3.895
xgobi.FCS	3.715	0.163	3.881