BioC 3.0: CHECK report for flowPlots on perceval

Package: flowPlots

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPlots_1.14.0.tar.gz

StartedAt: 2015-04-10 01:30:24 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:31:18 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 54.6 seconds

RetCode: 0

Status:  OK

CheckDir: flowPlots.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowPlots_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/flowPlots.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.14.0’
* 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 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/9s] 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 loading without being on the library search path ... 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.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
StackedData-class 8.411  0.045   8.484
* 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
* DONE

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.206	0.007	0.220
StackedData-class	8.411	0.045	8.484
adultsNeonates	0.001	0.001	0.002
computeMarginalData-methods	2.006	0.005	2.011
computeMarkers-methods	0.001	0.000	0.002
computePFDData-methods	1.739	0.006	1.749
computePFDGroupStatsList	0.285	0.015	0.353
computePFDPartsData-methods	2.468	0.013	2.482
computeProfileData-methods	2.232	0.009	2.241
legendPFDStatsGroupNames	0.114	0.003	0.193
makeBarplotData	0.013	0.001	0.224
makeDataList	0.050	0.002	0.060
makeTernaryData	0.123	0.004	0.191
marginalDF	0.002	0.001	0.002
marginalData-methods	0.003	0.001	0.003
markerMatrix	0.003	0.001	0.003
markers-methods	0.002	0.001	0.003
pfdDF	0.002	0.000	0.002
pfdData-methods	0.004	0.001	0.005
pfdPartsData-methods	0.004	0.001	0.005
pfdPartsList	0.002	0.001	0.002
profileDF	0.002	0.000	0.003
profileData-methods	0.003	0.000	0.003
readStackedData-methods	0.039	0.003	0.041
stackedData-methods	0.066	0.004	0.072