Package: flowMerge

Version: 2.28.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowMerge_2.28.0.tar.gz

StartedAt: 2018-10-16 00:26:28 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 00:27:44 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 75.7 seconds

RetCode: 0

Status:  OK

CheckDir: flowMerge.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings flowMerge_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/flowMerge.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘2.28.0’
* 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 ... 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
.compMD: no visible global function definition for ‘mahalanobis’
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 : <anonymous>: no visible global function definition for ‘rgb’
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<-’
flagOutliers,flowMerge: no visible global function definition for ‘qf’
Undefined global functions or variables:
  %do% %dopar% clusterEvalQ clusterMap foreach mahalanobis nodeData<-
  nodeDataDefaults<- nodeRenderInfo<- qf rgb subGraph
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "mahalanobis", "qf")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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-3.7-bioc/meat/flowMerge.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL flowMerge
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘flowMerge’ ...
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowMerge)

name	user	system	elapsed
NENT	0.000	0.000	0.001
fitPiecewiseLinreg	0.004	0.000	0.001
flowClust.res	0.004	0.000	0.001
flowMerge-package	0.000	0.000	0.001
flowObj	0.000	0.000	0.001
map	0.008	0.004	0.011
merge-methods	0.004	0.000	0.002
merge	0.004	0.000	0.000
pFlowMerge	0.008	0.000	0.006
plot-methods	0.000	0.000	0.001
updateU	0.000	0.000	0.001