BioC 2.13: CHECK report for flowPlots on perceval

Package: flowPlots

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPlots_1.10.0.tar.gz

StartedAt: 2014-04-05 01:17:13 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 01:18:13 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 60.2 seconds

RetCode: 0

Status:  OK

CheckDir: flowPlots.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowPlots.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowPlots’ version ‘1.10.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowPlots’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘flowPlots.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [29s/30s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
StackedData-class 13.346  0.124  13.829
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/flowPlots.Rcheck/00check.log’
for details.

* installing *source* package ‘flowPlots’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowPlots)

name	user	system	elapsed
GroupListBoxplot	0.235	0.016	0.253
StackedData-class	13.346	0.124	13.829
adultsNeonates	0.006	0.000	0.007
computeMarginalData-methods	2.936	0.024	3.005
computeMarkers-methods	0.01	0.00	0.01
computePFDData-methods	2.775	0.033	2.876
computePFDGroupStatsList	0.316	0.016	0.423
computePFDPartsData-methods	3.849	0.029	3.931
computeProfileData-methods	3.575	0.030	3.684
legendPFDStatsGroupNames	0.148	0.004	0.156
makeBarplotData	0.024	0.002	0.026
makeDataList	0.066	0.002	0.069
makeTernaryData	0.138	0.005	0.144
marginalDF	0.089	0.001	0.090
marginalData-methods	0.014	0.004	0.018
markerMatrix	0.008	0.002	0.010
markers-methods	0.012	0.002	0.014
pfdDF	0.005	0.000	0.006
pfdData-methods	0.014	0.000	0.014
pfdPartsData-methods	0.013	0.004	0.017
pfdPartsList	0.005	0.002	0.007
profileDF	0.007	0.002	0.009
profileData-methods	0.012	0.001	0.012
readStackedData-methods	0.050	0.002	0.053
stackedData-methods	0.085	0.008	0.097