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###
### Running command:
###
###   /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_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/netbiov.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netbiov/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netbiov’ version ‘1.34.0’
* 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 ... OK
* 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) 
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
> 
> ### 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/netbiov.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netbiov
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘netbiov’ ...
** 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 (netbiov)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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.

> require("RUnit")
Loading required package: RUnit
> require("netbiov")
Loading required package: netbiov
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

> 
> pattern="^test_.*\\.R$"
> runitDirs <- c(".")
> TEST_DATA_DIR <- "data"
> BiocGenerics:::testPackage("netbiov")
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...


RUNIT TEST PROTOCOL -- Wed Oct 18 11:15:32 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
netbiov RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> suite <- defineTestSuite(name="NetBioV Suite",
+                          dirs=runitDirs,
+                          testFileRegexp=pattern,
+                          rngKind="default",
+                          rngNormalKind="default")
> result <- runTestSuite(suite)
> printTextProtocol(result)
RUNIT TEST PROTOCOL -- Wed Oct 18 11:15:32 2023 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
NetBioV Suite - 0 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: NetBioV Suite 
Test function regexp: ^test.+ 
Test file regexp: ^test_.*\.R$ 
Involved directory: 
. 
no test files 
> 
> proc.time()
   user  system elapsed 
  9.428   0.459  15.173