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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNetStat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNetStat_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNetStat.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNetStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BioNetStat’ version ‘1.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BioNetStat’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.9Mb
    shiny     1.9Mb
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘RColorBrewer’ ‘RJSONIO’ ‘ggplot2’ ‘knitr’ ‘markdown’
  ‘pheatmap’ ‘plyr’ ‘rmarkdown’ ‘stats’ ‘utils’ ‘whisker’ ‘yaml’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘DT’ ‘shiny’ ‘shinyBS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
adjacencyMatrix : <anonymous>: no visible global function definition
  for ‘cor’
adjacencyMatrix : <anonymous>: no visible global function definition
  for ‘p.adjust’
betweennessCentralityTest: no visible global function definition for
  ‘bplapply’
betweennessCentralityVertexTest: no visible global function definition
  for ‘bplapply’
closenessCentralityTest: no visible global function definition for
  ‘bplapply’
closenessCentralityVertexTest: no visible global function definition
  for ‘bplapply’
clusteringCoefficientTest : <anonymous>: no visible global function
  definition for ‘dist’
clusteringCoefficientTest : <anonymous> : <anonymous>: no visible
  global function definition for ‘dist’
clusteringCoefficientTest: no visible global function definition for
  ‘bplapply’
clusteringCoefficientVertexTest: no visible global function definition
  for ‘bplapply’
degreeCentralityTest: no visible global function definition for
  ‘bplapply’
degreeCentralityVertexTest: no visible global function definition for
  ‘bplapply’
degreeDistributionTest: no visible global function definition for
  ‘bplapply’
diffNetAnalysis: no visible binding for global variable ‘expr’
diffNetAnalysis: no visible global function definition for ‘p.adjust’
doLabels: no visible global function definition for ‘read.csv’
edgeBetweennessEdgeTest: no visible global function definition for
  ‘bplapply’
edgeBetweennessTest: no visible global function definition for
  ‘bplapply’
edgesResInt : <anonymous>: no visible global function definition for
  ‘dist’
eigenvectorCentralityTest: no visible global function definition for
  ‘bplapply’
eigenvectorCentralityVertexTest: no visible global function definition
  for ‘bplapply’
gaussianDensity: no visible global function definition for ‘bw.nrd0’
gaussianDensity: no visible global function definition for ‘density’
pathPlot: no visible binding for global variable ‘median’
readVarFile: no visible global function definition for ‘read.table’
resInt : <anonymous>: no visible global function definition for ‘dist’
retEdgesTable: no visible global function definition for ‘p.adjust’
retTable: no visible global function definition for ‘p.adjust’
spectralDistributionTest: no visible global function definition for
  ‘bplapply’
spectralEntropyTest: no visible global function definition for
  ‘bplapply’
var.list: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate bplapply bw.nrd0 cor density dist expr median p.adjust
  read.csv read.table
Consider adding
  importFrom("stats", "aggregate", "bw.nrd0", "cor", "density", "dist",
             "median", "p.adjust")
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) centralityPathPlot.Rd:47: Escaped LaTeX specials: \#
* 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 ... ERROR
Running examples in ‘BioNetStat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edgeTest
> ### Title: Edge score equality test
> ### Aliases: edgeTest edgeBetweennessEdgeTest
> 
> ### ** Examples
> 
> set.seed(1)
> expr <- as.data.frame(matrix(rnorm(120),40,30))
> labels<-data.frame(code=rep(0:3,10),names=rep(c("A","B","C","D"),10))
> adjacencyMatrix1 <- adjacencyMatrix(method="spearman", association="pvalue",
+  threshold="fdr", thr.value=0.05, weighted=FALSE)
> # The numPermutations number is 1 to do a faster example, but we advise to use unless 1000 permutations in real analysis
> 
> # Edge betweenness centrality test
> diffNetAnalysis(method=edgeBetweennessEdgeTest, varFile=expr, labels=labels, varSets=NULL,
+  adjacencyMatrix=adjacencyMatrix1, numPermutations=1, print=TRUE, resultsFile=NULL,
+   seed=NULL, min.vert=5, option=NULL)
Testing all (1 of 1)
Error:
! The `edges` argument of `as_adjacency_matrix()` was deprecated in
  igraph 2.0.0 and is now defunct.
Backtrace:
     ▆
  1. └─BioNetStat::diffNetAnalysis(...)
  2.   └─BioNetStat (local) method(...)
  3.     └─BioNetStat:::edgesResEdgesInt(A, expr, weighted, igraph::edge_betweenness)
  4.       └─base::lapply(...)
  5.         └─BioNetStat (local) FUN(X[[i]], ...)
  6.           ├─base::as.matrix(as_adj(x, edges = T, type = "lower"))
  7.           └─igraph::as_adj(x, edges = T, type = "lower")
  8.             └─lifecycle::deprecate_stop("2.0.0", "as_adjacency_matrix(edges = )")
  9.               └─lifecycle:::deprecate_stop0(msg)
 10.                 └─rlang::cnd_signal(...)
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, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNetStat.Rcheck/00check.log’
for details.

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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNetStat
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BioNetStat’ ...
** 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
Warning in fun(libname, pkgname) :
  Package 'BioNetStat' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'BioNetStat' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (BioNetStat)