BioC 2.11: CHECK report for flowStats on perceval

Package: flowStats

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowStats_1.16.0.tar.gz

StartedAt: 2013-03-24 23:30:09 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:37:18 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 428.4 seconds

RetCode: 0

Status: OK

CheckDir: flowStats.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/flowStats.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '1.16.0'
* 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 for left-over 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
%in%,flowFrame-lymphFilter: warning in lymphGate(x, channels =
  parameters(table), preselection = pre, scale = table@scale, bwFac =
  table@bwFac, filterId = table@filterId, eval = TRUE, plot = FALSE):
  partial argument match of 'eval' to 'evaluate'
.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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
warpSet      49.342 24.686  77.493
gaussNorm    16.230  4.088  21.241
lymphGate    16.006  3.771  20.999
gpaSet        9.669  2.271  12.198
quadrantGate  8.699  3.180  12.661
density1d     8.644  2.579  11.532
rangeGate     7.367  2.738  10.657
autoGate      6.490  0.535   7.166
* 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
  '/Users/biocbuild/bbs-2.11-bioc/meat/flowStats.Rcheck/00check.log'
for details.

* installing *source* package 'flowStats' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
   'GettingStartedWithFlowStats.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'plot' when loading 'graphics'

* DONE (flowStats)

name	user	system	elapsed
autoGate	6.490	0.535	7.166
binByRef	1.367	0.266	1.690
calcPBChiSquare	1.305	0.219	1.584
calcPearsonChi	1.428	0.225	1.742
curvPeaks	1.247	0.259	1.555
density1d	8.644	2.579	11.532
gaussNorm	16.230	4.088	21.241
gpaSet	9.669	2.271	12.198
iProcrustes	0.613	0.031	0.646
idFeaturesByBackgating	2.328	0.028	2.374
landmarkMatrix	1.895	0.492	2.418
lymphGate	16.006	3.771	20.999
plotBins	1.589	0.261	1.944
proBin	0.898	0.147	1.062
quadrantGate	8.699	3.180	12.661
rangeGate	7.367	2.738	10.657
warpSet	49.342	24.686	77.493

Summary

Command output