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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:flowMerge.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings flowMerge_2.54.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/flowMerge.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘flowMerge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowMerge’ version ‘2.54.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/flowMerge.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL flowMerge
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)