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BioC 3.0: CHECK report for flowPlots on perceval

This page was generated on 2015-04-10 09:55:42 -0700 (Fri, 10 Apr 2015).

Package 316/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowPlots 1.14.0
N. Hawkins
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/flowPlots
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

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

Command output

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


* 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.

flowPlots.Rcheck/00install.out:

* 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)

flowPlots.Rcheck/flowPlots-Ex.timings:

nameusersystemelapsed
GroupListBoxplot0.2060.0070.220
StackedData-class8.4110.0458.484
adultsNeonates0.0010.0010.002
computeMarginalData-methods2.0060.0052.011
computeMarkers-methods0.0010.0000.002
computePFDData-methods1.7390.0061.749
computePFDGroupStatsList0.2850.0150.353
computePFDPartsData-methods2.4680.0132.482
computeProfileData-methods2.2320.0092.241
legendPFDStatsGroupNames0.1140.0030.193
makeBarplotData0.0130.0010.224
makeDataList0.0500.0020.060
makeTernaryData0.1230.0040.191
marginalDF0.0020.0010.002
marginalData-methods0.0030.0010.003
markerMatrix0.0030.0010.003
markers-methods0.0020.0010.003
pfdDF0.0020.0000.002
pfdData-methods0.0040.0010.005
pfdPartsData-methods0.0040.0010.005
pfdPartsList0.0020.0010.002
profileDF0.0020.0000.003
profileData-methods0.0030.0000.003
readStackedData-methods0.0390.0030.041
stackedData-methods0.0660.0040.072