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### Running command:
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###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:conclus.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings conclus_1.3.1.tar.gz
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/conclus.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'conclus/DESCRIPTION' ... OK
* this is package 'conclus' version '1.3.1'
* 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 'conclus' 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 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 ... WARNING
'::' or ':::' import not declared from: 'DT'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.removeNoSymbol: no visible binding for global variable 'SYMBOL'
Undefined global functions or variables:
  SYMBOL
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'clusterCellsInternal,scRNAseq-method':
clusterCellsInternal
  Code: function(theObject, clusterNumber = NULL, deepSplit = 4, cores
                 = 2, clusteringMethod = "ward.D2")
  Docs: function(theObject, clusterNumber = 0, deepSplit = 4, cores =
                 2, clusteringMethod = "ward.D2")
  Mismatches in argument default values:
    Name: 'clusterNumber' Code: NULL Docs: 0

Codoc mismatches from documentation object 'normaliseCountMatrix,scRNAseq-method':
normaliseCountMatrix
  Code: function(theObject, sizes = c(20, 40, 60, 80, 100), rowdata =
                 NULL, coldata = NULL, alreadyCellFiltered = FALSE,
                 runQuickCluster = TRUE, info = TRUE, removeNoSymbol =
                 FALSE)
  Docs: function(theObject, sizes = c(20, 40, 60, 80, 100), rowdata =
                 NULL, coldata = NULL, alreadyCellFiltered = FALSE,
                 runQuickCluster = TRUE, info = TRUE)
  Argument names in code not in docs:
    removeNoSymbol

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'getters'
  'cluster'

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 files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'conclus-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addClustering,scRNAseq-method
> ### Title: addClustering
> ### Aliases: addClustering,scRNAseq-method addClustering
> 
> ### ** Examples
> 
> ## Object scr containing the results of previous steps
> load(system.file("extdata/scrFull.Rdat", package="conclus"))
> 
> ## Retrieving the table indicating to which cluster each cell belongs
> clustCellsDf <- retrieveTableClustersCells(scr)
Error in validObject(theObject) : 
  invalid class "scRNAseq" object: slots in class definition but not in object: "topMarkers"
Calls: retrieveTableClustersCells -> retrieveTableClustersCells -> validObject
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'test-all.R'
 ERROR
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
    3. |   +-testthat .capture(...)
    4. |   | \-base::withCallingHandlers(...)
    5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. +-conclus::`setGenesInfos<-`(`*tmp*`, value = `<df[,12]>`)
    7. \-conclus::`setGenesInfos<-`(`*tmp*`, value = `<df[,12]>`)
    8.   \-methods::validObject(theObject)
    9.     +-methods anyStrings(validityMethod(object))
   10.     | \-base::isTRUE(x)
   11.     \-conclus validityMethod(object)
   12.       \-conclus:::.testGenesInfosSlot(object)
   13.         \-conclus:::checkGenesInfos(genesInfos, species, clustersSimiliratyOrdered)
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 76 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 3 WARNINGs, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/conclus.Rcheck/00check.log'
for details.