##############################################################################
##############################################################################
###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL conclus
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'conclus' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'conclus'
    finding HTML links ... done
    Dbscan-class                            html  
    Tsne-class                              html  
    addClustering-scRNAseq                  html  
    calculateClustersSimilarity-scRNAseq    html  
    clusterCellsInternal-scRNAseq           html  
    conclusCacheClear                       html  
    constructors                            html  
    exportResults-scRNAseq                  html  
    generateTSNECoordinates-scRNAseq        html  
    getters                                 html  
    loadDataOrMatrix                        html  
    normaliseCountMatrix-scRNAseq           html  
    plotCellHeatmap                         html  
    plotCellSimilarity-scRNAseq             html  
    plotClusteredTSNE-scRNAseq              html  
    plotClustersSimilarity                  html  
    plotGeneExpression-scRNAseq             html  
    rankGenes-scRNAseq                      html  
    retrieveFromGEO                         html  
    retrieveGenesInfo-scRNAseq              html  
    retrieveTableClustersCells-scRNAseq     html  
    retrieveTopClustersMarkers-scRNAseq     html  
    runCONCLUS                              html  
    runDBSCAN-scRNAseq                      html  
    scRNAseq-class                          html  
    setters                                 html  
    testClustering-scRNAseq                 html  
** 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 (conclus)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("conclus")


Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

> test_check("conclus")
[ FAIL 4 | WARN 1 | SKIP 0 | PASS 76 ]

== Failed tests ================================================================
-- Error (test_getters.R:89:5): getClustersMarkers works properly --------------
Error in `getClustersMarkers(scr)`: could not find function "getClustersMarkers"
Backtrace:
    x
 1. \-testthat::expect_equal(getClustersMarkers(scr), df) at test_getters.R:89:4
 2.   \-testthat::quasi_label(enquo(object), label, arg = "object")
 3.     \-rlang::eval_bare(expr, quo_get_env(quo))
-- Error (test_scRNAseq-methods.R:55:1): (code run outside of `test_that()`) ---
Error in `ans[ypos] <- rep(yes, length.out = len)[ypos]`: replacement has length zero
Backtrace:
    x
 1. +-conclus::normaliseCountMatrix(...) at test_scRNAseq-methods.R:55:0
 2. \-conclus::normaliseCountMatrix(...)
 3.   \-base::ifelse(...)
-- Error (test_setters.R:251:5): clustersMarkers works properly ----------------
Error in `setClustersMarkers(scr) <- newDF`: could not find function "setClustersMarkers<-"
-- Failure (test_setters.R:314:5): genesInfos works properly -------------------
`setGenesInfos(scr) <- wrongDF` threw an error with unexpected message.
Expected match: "The genesInfos data frame should have the columns: uniprot_gn_symbol;clusters;external_gene_name;go_id;entrezgene_description;gene_biotype;chromosome_name;Symbol;ensembl_gene_id;entrezgene_id;uniprot_gn_id;mgi_description;mgi_id"
Actual message: "The genesInfos data frame should have the columns: uniprot_gn_symbol;clusters;go_id;entrezgene_description;gene_biotype;chromosome_name;Symbol;ensembl_gene_id;entrezgene_id;uniprot_gn_id;mgi_description;mgi_id"
Backtrace:
     x
  1. +-testthat::expect_error(setGenesInfos(scr) <- wrongDF, regexp = expM) at test_setters.R:314:4
  2. | \-testthat:::quasi_capture(...)
  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