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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netbiov.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netbiov_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/netbiov.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netbiov/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netbiov’ version ‘1.32.0’
* 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 ‘netbiov’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.NetworkSperical plot.NetworkSperical.startSet
  plot.abstract.module plot.abstract.nodes plot.modules plot.netbiov
  plot.spiral.graph
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.edgeCol: no visible global function definition for ‘colors’
.get.coord.abstract : dst: no visible global function definition for
  ‘dist’
.get.coord.mod : dst: no visible global function definition for ‘dist’
.get.coord.mod_abs : dst: no visible global function definition for
  ‘dist’
.getalllevels: no visible global function definition for ‘pdf’
.getalllevels: no visible global function definition for ‘dev.off’
.getcrd.mod : dst: no visible global function definition for ‘dist’
.getcrd.mod: no visible global function definition for ‘rnorm’
.getcrd.mod.nodes : dst: no visible global function definition for
  ‘dist’
.getcrd.mod_abs : dst: no visible global function definition for ‘dist’
.getcrd.mod_abs: no visible global function definition for ‘rnorm’
.getcrd.mod_mst : dst: no visible global function definition for ‘dist’
.getcrd.mod_mst: no visible global function definition for ‘rnorm’
.set.mst.node.col: no visible global function definition for
  ‘heat.colors’
.set.mst.node.col_mod: no visible global function definition for
  ‘heat.colors’
.set.rank.abstract: no visible global function definition for ‘colors’
.set.rank.abstract: no visible global function definition for ‘hist’
.set.rank.abstract: no visible global function definition for
  ‘heat.colors’
.set.rank.mod: no visible global function definition for ‘hist’
.set.rank.mod: no visible global function definition for ‘colors’
.set.rank.mod: no visible global function definition for ‘heat.colors’
.set.rank.mod_abs: no visible global function definition for ‘hist’
.set.rank.mod_abs: no visible global function definition for ‘colors’
.set.rank.mod_abs: no visible global function definition for
  ‘heat.colors’
.set.rank.nodes: no visible global function definition for ‘hist’
.set.rank.nodes: no visible global function definition for ‘colors’
.set.rank.nodes: no visible global function definition for
  ‘heat.colors’
.set.rank.spiral: no visible global function definition for ‘hist’
.set.rank.spiral: no visible global function definition for ‘colors’
.set.rank.spiral: no visible global function definition for
  ‘heat.colors’
.set.split.vertex.color: no visible global function definition for
  ‘colors’
level.plot: no visible global function definition for ‘colors’
plot.NetworkSperical: no visible global function definition for
  ‘colors’
plot.NetworkSperical: no visible global function definition for
  ‘palette’
plot.NetworkSperical.startSet: no visible global function definition
  for ‘colors’
plot.NetworkSperical.startSet: no visible global function definition
  for ‘palette’
plot.netbiov: no visible global function definition for ‘par’
plot.spiral.graph : dst: no visible global function definition for
  ‘dist’
tkplot.netbiov: no visible global function definition for ‘par’
Undefined global functions or variables:
  colors dev.off dist heat.colors hist palette par pdf rnorm
Consider adding
  importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette",
             "pdf")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "dist", "rnorm")
to your NAMESPACE file.
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'level.plot':
  ‘...’

Documented arguments not in \usage in documentation object 'mst.plot':
  ‘...’

Documented arguments not in \usage in documentation object 'mst.plot.mod':
  ‘...’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... ERROR
Running examples in ‘netbiov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: level.plot
> ### Title: Exploratory visualization of information spread of biological
> ###   networks
> ### Aliases: level.plot
> 
> ### ** Examples
> 
> data("PPI_Athalina")
> 
> ### Example 1 #####
> #####% 5 initial nodes are picked randomly #####
> id <- level.plot(g1, init_nodes =5 ,tkplot=FALSE) 
> 
> ### Example 2 #####
> #####% initial nodes are given as an input #####
> id <- level.plot(g1, initial_nodes =c(1,4,5,7,9,11,25,27,29,100,101),
+ tkplot=FALSE) 
> 
> ### Example 3 #####
> #####% width of each level is same #####
> id <- level.plot(g1, initial_nodes 
+ =c(1,4,5,7,9,11,25,27,29,100,101), 
+ level.spread = TRUE,tkplot=FALSE) 
> 
> ### Example 4 #####
> #####% plot of graph when nodes are not arranged based on the degree #####
> id <- level.plot(g1, initial_nodes 
+ =c(1,4,5,7,9,11,25,27,29,100,101),
+ order_degree= NULL, level.spread = TRUE,
+ tkplot=FALSE) 
> 
> ### Example 5 #####
> #####% plot of graph when nodes are not arranged based on the degree #####
> id <- level.plot(g1, initial_nodes 
+ =c(1,4,5,7,9,11,25,27,29,100,101),
+ order_degree= NULL, level.spread = TRUE,
+ tkplot=FALSE) 
> 
> ### Example 6 #####
> ###% plot of graph using a forcebased algorithm 
> ###in igraph package #####
> xx <- level.plot(g1, layout.function=layout.reingold.tilford,
+ initial_nodes=c(1,4,5,7,9,11,25,27,29,100,101))
> 
> xx <- level.plot(g1, layout.function=layout.fruchterman.reingold,type=2, 
+ init_nodes=20)
> 
> xx <- level.plot(g1, layout.function=layout.kamada.kawai,
+ type=1, init_nodes=20)
> 
> ### Example 7 #####
> ## Shortest path between initial set of nodes at level '0'
> ## to a set of nodes with vertex id 10, 1000, 1001, 1002 ##%
> id <- level.plot(g1, initial_nodes=c(101,1,5,7),
+ vertex.colors=c("white", "white", "white"),
+ edge.col=c("grey", "grey", "grey", "grey"),
+ nodeset= list(c(101,1,5,7),c(10,1000,1001,1002)),
+ tkplot=FALSE, level.spread=TRUE,
+ order_degree=NULL)
> 
> ### Example 8 #####
> ###  A directed network is plotted with level.plot function ##%
> g <- barabasi.game(300, power=0)
Error in barabasi.game(300, power = 0) : 
  At core/games/barabasi.c:556 : Preferential attachment exponent must be positive, got 0. Invalid value
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 ERROR, 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/netbiov.Rcheck/00check.log’
for details.