Package: flowStats

Version: 1.14.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings flowStats_1.14.0.tar.gz

StartedAt: 2012-04-01 00:56:49 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 01:00:09 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 200.4 seconds

RetCode: 0

Status:  OK

CheckDir: flowStats.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/flowStats.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '1.14.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'flowStats' can be installed ... OK
* checking installed package size ... 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 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 ... NOTE
.plotGPAprocess: no visible binding for global variable 'whichS'
.plotGPAprocess: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'cluster'
.plotWorkFlow: no visible binding for global variable 'bogus'
.usingSVD: no visible binding for global variable 'params'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
* checking Rd files ... NOTE
prepare_Rd: normalizeGatingSet.Rd:53-55: Dropping empty section \note
prepare_Rd: normalizeGatingSet.Rd:47-49: Dropping empty section \references
prepare_Rd: normalizeGatingSet.Rd:62-63: Dropping empty section \examples
* 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... 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

NOTE: There were 2 notes.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/flowStats.Rcheck/00check.log'
for details.

* installing *source* package 'flowStats' ...
** R
** data
** inst
** preparing package for lazy loading
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

--------

for references have a look at
citation('robCompositions')    
--------

** help
*** installing help indices
** building package indices
** installing vignettes
   'GettingStartedWithFlowStats.Rnw' 
** testing if installed package can be loaded
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

--------

for references have a look at
citation('robCompositions')    
--------


* DONE (flowStats)

name	user	system	elapsed
autoGate	3.384	0.064	3.484
binByRef	0.864	0.048	0.947
calcPBChiSquare	0.900	0.024	0.992
calcPearsonChi	0.940	0.036	1.015
curvPeaks	0.760	0.004	0.826
density1d	4.584	0.052	4.691
gaussNorm	10.473	0.044	10.557
gpaSet	6.157	0.020	6.238
iProcrustes	0.372	0.004	0.377
idFeaturesByBackgating	1.832	0.004	1.875
landmarkMatrix	1.348	0.024	1.411
lymphGate	10.328	0.032	10.403
plotBins	1.048	0.040	1.138
proBin	0.773	0.020	0.837
quadrantGate	6.364	0.044	6.458
rangeGate	4.556	0.036	4.638
warpSet	24.666	0.104	24.819