BioC 3.1: CHECK report for flowPlots on petty

Package: flowPlots

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings flowPlots_1.16.0.tar.gz

StartedAt: 2015-10-08 23:01:42 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:02:35 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 52.5 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 flowPlots_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/flowPlots.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.16.0’
* 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 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/3s] 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 ... [20s/20s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
StackedData-class 8.855  0.038   8.897
* 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

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.1-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	0.232	0.008	0.240
StackedData-class	8.855	0.038	8.897
adultsNeonates	0.002	0.000	0.003
computeMarginalData-methods	2.048	0.002	2.050
computeMarkers-methods	0.002	0.000	0.002
computePFDData-methods	2.098	0.004	2.108
computePFDGroupStatsList	0.546	0.012	0.642
computePFDPartsData-methods	2.289	0.020	2.310
computeProfileData-methods	2.514	0.025	2.542
legendPFDStatsGroupNames	0.157	0.003	0.159
makeBarplotData	0.014	0.001	0.016
makeDataList	0.071	0.002	0.087
makeTernaryData	0.133	0.003	0.136
marginalDF	0.001	0.001	0.002
marginalData-methods	0.004	0.001	0.005
markerMatrix	0.002	0.000	0.002
markers-methods	0.004	0.001	0.005
pfdDF	0.002	0.001	0.003
pfdData-methods	0.004	0.001	0.004
pfdPartsData-methods	0.005	0.001	0.006
pfdPartsList	0.005	0.001	0.007
profileDF	0.001	0.000	0.002
profileData-methods	0.004	0.001	0.005
readStackedData-methods	0.052	0.003	0.054
stackedData-methods	0.094	0.009	0.104