##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings flowMerge_2.53.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/flowMerge.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMerge’ version ‘2.53.0’
* 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 code 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: no visible global function definition for ‘nodes’
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<- nodes subGraph
* checking Rd files ... WARNING
checkRd: (7) NENT.Rd:22: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) checkForRemoteErrors.Rd:22: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) fitPiecewiseLinreg.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowMerge-class.Rd:53: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowMerge-package.Rd:29: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowMerge-package.Rd:29: Invalid email address: <raphael.gottardo@ircm.qc.ca>
checkRd: (7) flowMerge-package.Rd:31: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowObj-class.Rd:50: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowObj-class.Rd:50: Invalid email address: <raphael.gottardo@ircm.qc.ca>
checkRd: (7) flowObj.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) flowObj.Rd:23: Invalid email address: <raphael.gottardo@ircm.qc.ca>
checkRd: (7) initPFlowMerge.Rd:19: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) merge.Rd:26: Invalid email address: <greg.finak@ircm.qc.cq>
checkRd: (7) mergeClusters.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) mergeClusters2.Rd:23: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) pFlowClust.Rd:39: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (7) pFlowMerge.Rd:36: Invalid email address: <greg.finak@ircm.qc.ca>
checkRd: (-1) split-methods.Rd:12: Lost braces
    12 | \\item{x = "flowMerge", f = "missing"}{ Split a flowMerge object into its component clusters. }
       |       ^
checkRd: (-1) split-methods.Rd:12: Lost braces
    12 | \\item{x = "flowMerge", f = "missing"}{ Split a flowMerge object into its component clusters. }
       |                                       ^
checkRd: (7) updateU.Rd:21: Invalid email address: <greg.finak@ircm.qc.ca>
* 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 ... 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-3.20-bioc/meat/flowMerge.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL flowMerge
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘flowMerge’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (flowMerge)