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BioC 2.14: CHECK report for flowMap on zin2

This page was generated on 2014-10-08 08:50:14 -0700 (Wed, 08 Oct 2014).

Package 284/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMap 1.99.2
Chiaowen Joyce Hsiao
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowMap
Last Changed Rev: 93720 / Revision: 95116
Last Changed Date: 2014-08-31 08:12:28 -0700 (Sun, 31 Aug 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: flowMap
Version: 1.99.2
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings flowMap_1.99.2.tar.gz
StartedAt: 2014-10-07 23:34:44 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:35:54 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 70.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: flowMap.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings flowMap_1.99.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/flowMap.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMap’ version ‘1.99.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘ade4’ ‘doParallel’ ‘abind’ ‘reshape2’ ‘ggplot2’ ‘igraph’ ‘scales’
  ‘Matrix’ ‘gplots’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘flowMap’ can be installed ... [7s/7s] 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
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘igraph’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘abind’ ‘ade4’ ‘doParallel’ ‘ggplot2’ ‘gplots’ ‘igraph’
  ‘methods’ ‘reshape2’ ‘scales’
  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 ... NOTE
getFRest: no visible binding for global variable ‘i’
* 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 ... WARNING
Undocumented arguments in documentation object 'getFRest'
  ‘ncores’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/3s] OK
* 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

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-bioc/meat/flowMap.Rcheck/00check.log’
for details.

flowMap.Rcheck/00install.out:

* installing *source* package ‘flowMap’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowMap)

flowMap.Rcheck/flowMap-Ex.timings:

nameusersystemelapsed
frstats-class000
getFR000
getFRest000