##############################################################################
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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:scTreeViz.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings scTreeViz_1.1.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/scTreeViz.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 'scTreeViz/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scTreeViz' version '1.1.1'
* 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 'scTreeViz' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.generate_hierarchy_tree: no visible binding for global variable
  'otu_index'
.generate_leaf_of_table: no visible binding for global variable 'leaf'
.generate_leaf_of_table: no visible binding for global variable
  'otu_index'
.generate_leaf_of_table: no visible binding for global variable 'id'
.generate_node_ids : <anonymous>: no visible global function definition
  for '.'
.generate_node_ids : <anonymous>: no visible binding for global
  variable 'otu_index'
.generate_nodes_table: no visible binding for global variable 'id'
.generate_nodes_table: no visible binding for global variable 'lineage'
.generate_nodes_table: no visible binding for global variable
  'node_label'
.generate_nodes_table: no visible binding for global variable 'level'
.preprocessAndCreateTreeViz: no visible global function definition for
  'chracter'
getNodes,TreeIndex: no visible binding for global variable 'level'
getNodes,TreeIndex: no visible binding for global variable 'id'
splitAt,TreeIndex: no visible binding for global variable 'level'
splitAt,TreeIndex: no visible binding for global variable 'id'
splitAt,TreeIndex: no visible binding for global variable 'lineage'
splitAt,TreeIndex: no visible binding for global variable 'leaf'
splitAt,TreeIndex: no visible binding for global variable 'otu_index'
splitAt,TreeIndex: no visible global function definition for '.'
splitAt,TreeIndex: no visible binding for global variable 'node_label'
Undefined global functions or variables:
  . chracter id leaf level lineage node_label otu_index
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
TreeIndex-methods 18.11   1.69   19.75
TreeViz            9.19   0.35    9.53
TreeIndex          9.09   0.12    9.22
createFromSCE      8.28   0.12    8.45
* 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: 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/scTreeViz.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL scTreeViz
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'scTreeViz' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
Warning message:
replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData' 
** help
*** installing help indices
  converting help for package 'scTreeViz'
    finding HTML links ... done
    ClusterHierarchy-class                  html  
    ClusterHierarchy                        html  
    EpivizTreeData-class                    html  
    TreeIndex-class                         html  
    TreeIndex-methods                       html  
    TreeIndex                               html  
    TreeViz-class                           html  
    TreeViz-methods                         html  
    TreeViz                                 html  
    TreeVizApp-class                        html  
    createFromSCE                           html  
    createFromSeurat                        html  
    createTreeViz                           html  
    dot-generate_hierarchy_tree             html  
    dot-generate_leaf_of_table              html  
    dot-generate_node_ids                   html  
    dot-generate_nodes_table                html  
    dot-replaceNAFeatures                   html  
    set_gene_list                           html  
    startTreeviz                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData'
** testing if installed package keeps a record of temporary installation path
* DONE (scTreeViz)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'InPAS' is missing or broken
 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(scTreeViz)
Loading required package: epivizr
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Warning message:
replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'epivizrData' 
> 
> test_check("scTreeViz")
[1] "root"       "3.cluster3" "5.cluster5" "6.cluster6" "samples"   
[1] "root"       "3.cluster3" "5.cluster5"
[1] "1.cluster1" "2.cluster2" "3.cluster3" "samples"   
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 7 ]

== Skipped tests ===============================================================
* conflict between new Seurat and Summarized Experiment (1)
* need data here (1)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
  17.34    1.06   18.37