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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:flowStats.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings flowStats_4.23.0.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/flowStats.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘flowStats/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowStats’ version ‘4.23.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Greg Finak <greg@ozette.com>, Mike Jiang <mike@ozette.com>’

The maintainer field is invalid or specifies more than one person

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘Lazyload’ ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = "Florian",
                      family = "Hahne",
                      role = "aut"),
               person(given = "Nishant",
                      family = "Gopalakrishnan",
                      role = "aut"),
               person(given = c("Alireza", "Hadj"),
                      family = "Khodabakhshi",
                      role = "aut"),
               person(given = "Chao-Jen",
                      family = "Wong",
                      role = "aut"),
               person(given = "Kyongryun",
                      family = "Lee",
                      role = "aut"),
               person(given = "Greg",
                      family = "Finak",
                      role = "cre",
                      email = "greg@ozette.com"),
               person(given = "Mike",
                      family = "Jiang",
                      role = "cre",
                      email = "mike@ozette.com"))
as necessary.

The Title field should be in title case. Current version is:
  ‘Statistical methods for the analysis of flow cytometry data’
In title case that is:
  ‘Statistical Methods for the Analysis of Flow Cytometry Data’
* 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-3.23-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 use of S3 registration ... 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’

Non-topic package-anchored link(s) in Rd file 'landmarkMatrix.Rd':
  ‘[fda:fda-package]{fda}’

Non-topic package-anchored link(s) in Rd file 'warpSet.Rd':
  ‘[fda:fda-package]{fda}’

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 ... WARNING
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ... WARNING
Fatal error: cannot create 'R_TempDir'
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.
Fatal error: cannot create 'R_TempDir'
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking for unstated dependencies in examples ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking contents of ‘data’ directory ... NOTE
Output for data("BackGating", package = "flowStats"):
  Fatal error: cannot create 'R_TempDir'
Output for data("ITN", package = "flowStats"):
  Fatal error: cannot create 'R_TempDir'
* 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 sizes of PDF files under ‘inst/doc’ ...* 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-3.23-bioc-rapid/R/bin/R CMD INSTALL flowStats
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘flowStats’ ...
** this is package ‘flowStats’ version ‘4.23.0’
** 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)