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BioC 3.3: CHECK report for flowMerge on linux2.bioconductor.org

This page was generated on 2015-10-27 12:11:45 -0400 (Tue, 27 Oct 2015).

Package 362/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
flowMerge 2.19.0
Greg Finak
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowMerge
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: flowMerge
Version: 2.19.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowMerge_2.19.0.tar.gz
StartedAt: 2015-10-27 03:52:48 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 03:53:54 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 65.3 seconds
RetCode: 0
Status:  OK 
CheckDir: flowMerge.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowMerge_2.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowMerge.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMerge’ version ‘2.19.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘multicore’

Depends: includes the non-default packages:
  ‘graph’ ‘feature’ ‘flowClust’ ‘Rgraphviz’ ‘foreach’ ‘snow’
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 ‘flowMerge’ can be installed ... [6s/6s] 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
Packages in Depends field not imported from:
  ‘foreach’ ‘snow’
  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 ... NOTE
initPFlowMerge: no visible global function definition for
  ‘clusterEvalQ’
mergeClusters: no visible global function definition for ‘%dopar%’
mergeClusters: no visible global function definition for ‘foreach’
mergeClusters: no visible global function definition for ‘%do%’
pFlowClust : <anonymous>: no visible global function definition for
  ‘clusterMap’
pFlowClust: no visible global function definition for ‘clusterMap’
ptree: no visible global function definition for ‘subGraph’
ptree : <anonymous>: no visible global function definition for
  ‘nodeDataDefaults<-’
ptree : <anonymous>: no visible global function definition for
  ‘nodeData<-’
ptree : <anonymous>: no visible global function definition for
  ‘subGraph’
ptree : <anonymous>: no visible global function definition for
  ‘nodeRenderInfo<-’
Undefined global functions or variables:
  %do% %dopar% clusterEvalQ clusterMap foreach nodeData<-
  nodeDataDefaults<- nodeRenderInfo<- subGraph
* 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 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/flowMerge.Rcheck/00check.log’
for details.


flowMerge.Rcheck/00install.out:

* installing *source* package ‘flowMerge’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘merge’ from package ‘base’ in package ‘flowMerge’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowMerge)

flowMerge.Rcheck/flowMerge-Ex.timings:

nameusersystemelapsed
NENT0.0010.0000.000
fitPiecewiseLinreg0.0010.0000.000
flowClust.res0.0000.0000.001
flowMerge-package0.0010.0000.000
flowObj0.0010.0000.001
map0.0030.0000.003
merge-methods0.0010.0000.000
merge000
pFlowMerge0.0080.0080.017
plot-methods0.0010.0000.001
updateU0.0010.0000.001