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### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CytoML.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CytoML_2.8.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/CytoML.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CytoML/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CytoML' version '2.8.1'
* 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 whether package 'CytoML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      8.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods'
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  'RUnit' 'corpcor' 'openCyto' 'stats'
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  'ggcyto:::merge.quad.gates' 'lattice:::updateList'
  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
addCustomInfo: no visible global function definition for
  'gh_get_transformations'
addGate: no visible binding for global variable 'id'
addGate: no visible binding for global variable 'gate_id'
addGate: no visible binding for global variable 'fcs'
addGate: no visible binding for global variable 'fcs_file_id'
addGate: no visible binding for global variable 'gate_def'
addGate: no visible binding for global variable 'name'
ce_get_panels: no visible binding for global variable 'panel'
ce_get_panels: no visible binding for global variable 'n'
constructTree: no visible binding for global variable 'id'
constructTree: no visible binding for global variable 'name'
createTransformIdentifier: no visible global function definition for
  'slotNames'
cytobank_to_gatingset.cytobank_experiment: no visible binding for
  global variable 'desc'
diva_to_gatingset: no visible binding for global variable 'specimen'
diva_to_gatingset: no visible binding for global variable
  'sampleSelected'
diva_to_gatingset: no visible global function definition for
  'gh_apply_to_new_fcs'
export_comp_trans: no visible global function definition for
  'gh_get_compensations'
export_comp_trans: no visible global function definition for
  'gh_get_transformations'
export_gates_cytobank: no visible global function definition for
  'gs_get_pop_paths'
export_gates_cytobank: no visible global function definition for
  'gs_pop_get_gate'
extend.polygonGate: no visible binding for global variable '..dim'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'y'
extend.polygonGate : <anonymous>: no visible binding for global
  variable 'x'
extend.polygonGate: no visible binding for global variable 'id'
extend.polygonGate: no visible binding for global variable 'x'
extend.polygonGate: no visible binding for global variable 'y'
extend.polygonGate: no visible binding for global variable 'is.smaller'
flinTr: no visible global function definition for 'lintGml2'
fratioTr: no visible global function definition for 'ratiotGml2'
generate_trans: no visible global function definition for
  'flowjo_log_trans'
gs_compare_cytobank_counts: no visible binding for global variable
  'population'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent'
gs_compare_cytobank_counts: no visible binding for global variable
  'parent_count'
gs_compare_cytobank_counts: no visible global function definition for
  '.'
gs_compare_cytobank_counts: no visible binding for global variable
  'fcs_filename'
hyperlogTr: no visible global function definition for 'hyperlogtGml2'
open_cytobank_experiment: no visible global function definition for
  'unzip'
range.GatingHierarchy: no visible global function definition for
  'gh_get_transformations'
read.gatingML.cytobank: no visible binding for global variable 'id'
read.gatingML.cytobank: no visible binding for global variable
  'comp_ref'
transDg1polynomial: no visible global function definition for
  'dg1polynomial'
transEH: no visible global function definition for 'EHtrans'
transExponential: no visible global function definition for
  'exponential'
transHyperLog: no visible global function definition for 'hyperlog'
transHyperbolicSin: no visible global function definition for 'sinht'
transInvSplitScale: no visible global function definition for
  'invsplitscale'
transInverseHyperbolicSin: no visible global function definition for
  'asinht'
transLogarithm: no visible global function definition for 'logarithm'
transQuadratic: no visible global function definition for 'quadratic'
transRatio: no visible global function definition for 'ratio'
transSplitScale: no visible global function definition for 'splitscale'
transSquareroot: no visible global function definition for 'squareroot'
write.gatingML: no visible global function definition for 'sessionInfo'
xmlVertexNode : <anonymous>: no visible global function definition for
  'format_float'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_DecisionTreeGate:
  no visible binding for global variable 'expressionFilter'
identifyNode,http...www.isac.net.org.std.Gating.ML.v1.5.gating_PolytopeGate:
  no visible global function definition for 'polytopeGate'
identifyNode,http...www.isac.net.org.std.Gating.ML.v2.0.transformations_spectrumMatrix:
  no visible global function definition for 'pseudoinverse'
show,flowjo_workspace: no visible binding for global variable
  'groupName'
show,flowjo_workspace: no visible binding for global variable 'groupID'
Undefined global functions or variables:
  . ..dim EHtrans asinht comp_ref desc dg1polynomial exponential
  expressionFilter fcs fcs_file_id fcs_filename flowjo_log_trans
  format_float gate_def gate_id gh_apply_to_new_fcs
  gh_get_compensations gh_get_transformations groupID groupName
  gs_get_pop_paths gs_pop_get_gate hyperlog hyperlogtGml2 id
  invsplitscale is.smaller lintGml2 logarithm n name panel parent
  parent_count polytopeGate population pseudoinverse quadratic ratio
  ratiotGml2 sampleSelected sessionInfo sinht slotNames specimen
  splitscale squareroot unzip x y
Consider adding
  importFrom("methods", "slotNames")
  importFrom("utils", "sessionInfo", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... WARNING
Undocumented arguments in documentation object 'parseWorkspace'
  'backend_dir' 'backend'
Documented arguments not in \usage in documentation object 'parseWorkspace':
  'h5_dir'

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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently using $(BLAS_LIBS) without following $(FLIBS) in 'src/Makevars.in'
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/CytoML/libs/x64/CytoML.dll':
  Found '_assert', possibly from 'assert' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 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: 2 WARNINGs, 6 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/CytoML.Rcheck/00check.log'
for details.