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Package 354/444HostnameOS / ArchBUILDCHECKBUILD BIN
rflowcyt 1.23.0
N. LeMeur
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rflowcyt
Last Changed Rev: 52671 / Revision: 53825
Last Changed Date: 2011-02-14 09:56:37 -0800 (Mon, 14 Feb 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ OK ] OK 

Summary

Package: rflowcyt
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rflowcyt_1.23.0.tar.gz
StartedAt: 2011-03-17 17:18:05 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 17:22:54 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 289.0 seconds
RetCode: 0
Status:  OK 
CheckDir: rflowcyt.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/rflowcyt.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* 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 '1.23.0'
* 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 12.5Mb
  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 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

rflowcyt.Rcheck/00install.out:

* 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 1.1-00)
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 ...
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.1-00)

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)

rflowcyt.Rcheck/rflowcyt-Ex.timings:

nameusersystemelapsed
ContourScatterPlot4.4950.1144.684
FCS-class0.0720.0060.078
FCSgate-class0.0010.0000.001
FCSmetadata-class0.0150.0020.018
FCSsummary-class0.0010.0000.001
FHCRC.HVTNFCS0.2710.0060.277
ImageParCoord3.0180.0823.100
KS.flowcytest2.8650.0782.942
MODE0.0120.0000.012
PercentPos.FCS3.3840.0893.472
ProbBin.FCS3.0100.0823.092
ProbBin.flowcytest2.9450.0793.025
ROC.FCS0.0050.0010.020
VRC.HVTNFCS2.8580.0682.926
WLR.flowcytest2.8410.0672.907
add.parallel.coordinates0.2470.0020.250
add.parallelCoordinates0.3390.0050.343
boxplot.FCS8.4730.2869.823
breakpoints.ProbBin0.0070.0010.008
coerce-FCSformat0.0020.0000.002
convertS3toS40.0270.0020.028
createGate2.5530.4353.564
cytoSet-class0.3150.0190.404
emp.f0.0080.0010.011
extractGateHistory1.2790.2421.534
extractGatedData1.3810.2141.596
fcs.type0.0150.0020.017
gate.IPC2.8680.0782.946
get.h0.0380.0020.041
get.num.modes0.0790.0100.090
get.p1.1730.0241.197
legend.CSP3.5670.0933.661
make.grid8.7260.5369.261
pairs.CSP0.0030.0000.003
parallelCoordinates0.2460.0040.251
pkci2.flowcytest2.7250.0692.795
plot.ProbBin.FCS2.8350.0692.905
plot2sets.FCS0.0000.0010.000
plotECDF.FCS7.7020.2697.972
plotQA.FCS25.616 0.35825.974
plotdensity.FCS0.3190.0070.327
plotvar.FCS0.0030.0020.006
read.FCS0.0150.0010.016
read.series.FCS0.0760.0060.083
rect.box.idx0.0110.0010.021
runflowcytests2.7910.0772.868
showgate.FCS0.0020.0000.002
standard0.0010.0000.002
summary.ProbBin.FCS2.9110.0802.991
xgobi.FCS2.7410.0712.812