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### Running command:
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###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings flowStats_4.19.0.tar.gz
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/flowStats.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘4.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘flowStats’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/flowStats.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 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 ... WARNING
Missing or unexported object: ‘flowWorkspace::plotGate’
Missing object imported by a ':::' call: ‘flowWorkspace:::.isBooleanGate.graphNEL’
Unexported objects imported by ':::' calls:
  ‘flowCore:::checkClass’ ‘flowCore:::copyFlowSet’
  ‘flowCore:::findTimeChannel’ ‘flowCore:::inPolygon’
  ‘flowViz:::evalError’ ‘flowViz:::plotType’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.combinePriorsForChildNodes: no visible global function definition for
  ‘adj’
.combinePriorsForChildNodes: no visible global function definition for
  ‘nodeData’
.graph_parent: no visible global function definition for ‘ugraph’
.plotGPAprocess: no visible binding for global variable ‘whichS’
.plotGPAprocess: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘cluster’
.plotWorkFlow: no visible binding for global variable ‘bogus’
.usingSVD: no visible binding for global variable ‘params’
SimulateMixture: no visible global function definition for ‘rbox’
density1d_simple: no visible binding for global variable ‘y’
normQA: no visible binding for global variable ‘group’
normQA: no visible binding for global variable ‘hasPeak’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘adist’
Undefined global functions or variables:
  adist adj bogus cluster group hasPeak nodeData params rbox ugraph
  whichS y
Consider adding
  importFrom("utils", "adist")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'SimulateMixture.Rd':
  ‘flowClust’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SimulateMixture.Rd: flowClust
  curv1Filter-class.Rd: multipleFilterResult, flowFrame,
    parameterFilter-class, concreteFilter-class, filter-class, flowSet
  curv2Filter-class.Rd: multipleFilterResult, flowFrame,
    parameterFilter-class, concreteFilter-class, filter-class, flowSet
  norm2Filter-class.Rd: logicalFilterResult, flowFrame, flowSet,
    parameterFilter-class, concreteFilter-class, filter-class, Subset
  spillover-flowSet.Rd: compensate, read.FCS, flowSet
  spillover_match-flowSet.Rd: compensate
  spillover_ng-flowSet.Rd: compensate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'ellipse.Rd'
  ‘cov’ ‘centre’ ‘level’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... INFO
  Fatal error: cannot create 'R_TempDir'
* checking data for ASCII and uncompressed saves ... WARNING
  Fatal error: cannot create 'R_TempDir'
* checking files in ‘vignettes’ ...Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: inferior call failed
Execution halted

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL flowStats
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘flowStats’ ...
** this is package ‘flowStats’ version ‘4.19.0’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’
** testing if installed package keeps a record of temporary installation path
* DONE (flowStats)