BioC 2.12: CHECK report for flowStats on lamb2

Package: flowStats

Version: 1.17.1

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings flowStats_1.17.1.tar.gz

StartedAt: 2013-01-16 02:29:51 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:36:47 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 416.4 seconds

RetCode: 0

Status: OK

CheckDir: flowStats.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/flowStats.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘1.17.1’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowStats’ can be installed ... 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’
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
Examples with CPU or elapsed time > 5s
               user system elapsed
warpSet      54.075  0.196  54.274
gaussNorm    18.033  0.092  18.131
lymphGate    14.565  0.096  14.666
quadrantGate 10.696  0.132  10.842
gpaSet       10.364  0.064  10.429
density1d    10.061  0.080  10.152
rangeGate     8.817  0.116   8.937
autoGate      7.677  0.120   7.823
* 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/biocbuild/bbs-2.12-bioc/meat/flowStats.Rcheck/00check.log’
for details.

* installing *source* package ‘flowStats’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘GettingStartedWithFlowStats.Rnw’ 
** testing if installed package can be loaded

* DONE (flowStats)

name	user	system	elapsed
autoGate	7.677	0.120	7.823
binByRef	1.268	0.036	1.304
calcPBChiSquare	1.220	0.044	1.264
calcPearsonChi	1.292	0.052	1.345
curvPeaks	1.160	0.040	1.201
density1d	10.061	0.080	10.152
gaussNorm	18.033	0.092	18.131
gpaSet	10.364	0.064	10.429
iProcrustes	0.336	0.000	0.337
idFeaturesByBackgating	2.501	0.004	2.504
landmarkMatrix	1.700	0.028	1.727
lymphGate	14.565	0.096	14.666
plotBins	1.628	0.040	1.670
proBin	0.608	0.052	0.659
quadrantGate	10.696	0.132	10.842
rangeGate	8.817	0.116	8.937
warpSet	54.075	0.196	54.274

Summary

Command output