Package: flowMerge

Version: 2.30.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowMerge_2.30.1.tar.gz

StartedAt: 2019-04-15 23:58:27 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-16 00:00:10 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 103.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: flowMerge.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings flowMerge_2.30.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowMerge.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.30.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘doMC’ ‘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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowMerge.Rcheck/00install.out’ for details.
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/flowMerge.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL flowMerge
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘flowMerge’ ...
** R
** data
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (flowMerge)

name	user	system	elapsed
NENT	0.000	0.000	0.001
fitPiecewiseLinreg	0.001	0.000	0.001
flowClust.res	0	0	0
flowMerge-package	0	0	0
flowObj	0.000	0.001	0.001
map	0.011	0.001	0.012
merge-methods	0	0	0
merge	0.000	0.000	0.001
pFlowMerge	0.006	0.002	0.008
plot-methods	0	0	0
updateU	0.000	0.001	0.000