BioC 2.12: CHECK report for flowStats on pelham

Package: flowStats

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowStats_1.18.0.tar.gz

StartedAt: 2013-05-01 05:21:21 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:30:12 -0700 (Wed, 01 May 2013)

EllapsedTime: 531.4 seconds

RetCode: 0

Status: OK

CheckDir: flowStats.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/flowStats.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'flowStats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'flowStats' version '1.18.0'
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'flowStats' can be installed ... [31s/33s] OK
* checking installed package size ... OK
* checking package directory ... 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'
density1d_simple: no visible binding for global variable 'y'
normQA: no visible binding for global variable 'group'
normQA: no visible binding for global variable 'hasPeak'
* checking Rd files ... OK
* 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 ... [213s/222s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
warpSet   64.791 18.542  84.765
gaussNorm 22.054  2.900  26.162
lymphGate 18.238  2.359  20.793
density1d 14.856  2.071  19.833
rangeGate 11.120  2.131  13.433
gpaSet    10.979  1.522  12.809
autoGate   7.708  0.385   8.477
* 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-2.12-bioc/meat/flowStats.Rcheck/00check.log'
for details.

* installing *source* package 'flowStats' ...
** R
** data
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
Warning: replacing previous import 'plot' when loading 'graphics'
* DONE (flowStats)

name	user	system	elapsed
autoGate	7.708	0.385	8.477
binByRef	1.699	0.174	1.897
calcPBChiSquare	1.646	0.175	1.914
calcPearsonChi	1.757	0.182	2.006
curvPeaks	2.004	0.194	2.527
density1d	14.856	2.071	19.833
gaussNorm	22.054	2.900	26.162
gpaSet	10.979	1.522	12.809
iProcrustes	0.444	0.034	0.493
idFeaturesByBackgating	3.105	0.044	3.218
landmarkMatrix	2.089	0.419	2.559
lymphGate	18.238	2.359	20.793
normalize	0.005	0.010	0.015
plotBins	2.004	0.189	2.222
proBin	0.945	0.119	1.077
quadrantGate	0.012	0.029	0.042
rangeGate	11.120	2.131	13.433
singletGate	0.009	0.018	0.028
warpSet	64.791	18.542	84.765

Summary

Command output