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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:treekoR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings treekoR_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/treekoR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘treekoR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘treekoR’ version ‘1.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘treekoR’ 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 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 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
addFreqBars: no visible binding for global variable ‘freq’
addFreqBars: no visible binding for global variable ‘xmax’
addFreqBars: no visible binding for global variable ‘y’
addFreqBars: no visible binding for global variable ‘xmin’
addFreqBars: no visible binding for global variable ‘ymin’
addFreqBars: no visible binding for global variable ‘ymax’
addFreqBars: no visible binding for global variable ‘x_label’
addFreqBars: no visible binding for global variable ‘freq_label’
addHeatMap: no visible binding for global variable ‘variable’
addHeatMap: no visible binding for global variable ‘value’
addHeatMap: no visible binding for global variable ‘y’
addHeatMap: no visible binding for global variable ‘label’
addHeatMap: no visible binding for global variable ‘.’
addHeatMap: no visible binding for global variable ‘x’
colourTree: no visible binding for global variable ‘stat_parent’
colourTree: no visible binding for global variable ‘x’
colourTree: no visible binding for global variable ‘y’
colourTree: no visible binding for global variable ‘stat_total’
colourTree: no visible binding for global variable ‘label’
getCellGMeans: no visible binding for global variable ‘cluster_id’
getCellGMeans: no visible binding for global variable ‘sample_id’
getCellProp: no visible binding for global variable ‘cluster_id’
getCellProp: no visible binding for global variable ‘sample_id’
getCellProp: no visible binding for global variable ‘.’
getClusterTree: no visible binding for global variable ‘cluster_id’
plotInteractiveHeatmap: no visible binding for global variable ‘label’
plotInteractiveHeatmap: no visible binding for global variable ‘node’
plotSigScatter: no visible binding for global variable ‘stat_total’
plotSigScatter: no visible binding for global variable ‘stat_parent’
plotSigScatter: no visible binding for global variable ‘isTip’
plotSigScatter: no visible binding for global variable ‘label’
runEdgeRTests: no visible binding for global variable ‘PValue’
runEdgeRTests: no visible binding for global variable ‘logFC’
runEdgeRTests: no visible binding for global variable ‘node’
runEdgeRTests: no visible binding for global variable ‘stat_parent’
runEdgeRTests: no visible binding for global variable ‘pval_parent’
runEdgeRTests: no visible binding for global variable ‘FDR_parent’
runEdgeRTests: no visible binding for global variable ‘PValue_total’
runEdgeRTests: no visible binding for global variable ‘logFC_total’
runEdgeRTests: no visible binding for global variable ‘stat_total’
runEdgeRTests: no visible binding for global variable ‘pval_total’
runEdgeRTests: no visible binding for global variable ‘FDR_total’
runGLMMTests: no visible binding for global variable ‘isTip’
runGLMMTests: no visible binding for global variable ‘node’
Undefined global functions or variables:
  . FDR_parent FDR_total PValue PValue_total cluster_id freq freq_label
  isTip label logFC logFC_total node pval_parent pval_total sample_id
  stat_parent stat_total value variable x x_label xmax xmin y ymax ymin
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_testTree.R:31:1'): (code run outside of `test_that()`) ─────────
  Error in `rowMeans(dmat[labels == ordlabels[j], labels == labels[medoid2]])`: 'x' must be an array of at least two dimensions
  Backtrace:
      ▆
   1. └─treekoR::getClusterTree(exprs, clusters_str, hierarchy_method = "hopach") at test_testTree.R:31:1
   2.   └─treekoR::runHOPACH(...)
   3.     └─hopach::hopach(data, K = K, dmat = dist, kmax = kmax)
   4.       └─hopach::mssrundown(...)
   5.         └─hopach::mssnextlevel(...)
   6.           └─base::rowMeans(dmat[labels == ordlabels[j], labels == labels[medoid2]])
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/treekoR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL treekoR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘treekoR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (treekoR)

R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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(treekoR)
> 
> test_check("treekoR")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_testTree.R:31:1'): (code run outside of `test_that()`) ─────────
Error in `rowMeans(dmat[labels == ordlabels[j], labels == labels[medoid2]])`: 'x' must be an array of at least two dimensions
Backtrace:
    ▆
 1. └─treekoR::getClusterTree(exprs, clusters_str, hierarchy_method = "hopach") at test_testTree.R:31:1
 2.   └─treekoR::runHOPACH(...)
 3.     └─hopach::hopach(data, K = K, dmat = dist, kmax = kmax)
 4.       └─hopach::mssrundown(...)
 5.         └─hopach::mssnextlevel(...)
 6.           └─base::rowMeans(dmat[labels == ordlabels[j], labels == labels[medoid2]])

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted