Package: netbiov

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netbiov.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netbiov_1.17.0.tar.gz

StartedAt: 2019-04-09 02:30:33 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:35:03 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 269.9 seconds

RetCode: 0

Status:  OK

CheckDir: netbiov.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:netbiov.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings netbiov_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/netbiov.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.17.0’
* 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’
.ploteachstep: no visible global function definition for ‘plot’
.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.netbiov: no visible global function definition for ‘plot’
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 plot rnorm
Consider adding
  importFrom("grDevices", "colors", "dev.off", "heat.colors", "palette",
             "pdf")
  importFrom("graphics", "hist", "par", "plot")
  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 ... 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 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 ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
level.plot           82.418  1.709  85.434
plot.abstract.module 51.406  1.291  54.520
plot.modules         38.003  1.214  39.590
mst.plot             17.037  0.202  17.471
mst.plot.mod          5.958  0.184   6.194
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/netbiov.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL netbiov
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘netbiov’ ...
** 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
* DONE (netbiov)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")


RUNIT TEST PROTOCOL -- Tue Apr  9 02:34:48 2019 
*********************************************** 
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 -- Tue Apr  9 02:34:48 2019 
*********************************************** 
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 
 10.872   0.595  11.517 

name	user	system	elapsed
PPI_Athalina	0.022	0.004	0.027
level.plot	82.418	1.709	85.434
mst.plot	17.037	0.202	17.471
mst.plot.mod	5.958	0.184	6.194
plot.NetworkSperical	0.760	0.003	0.769
plot.NetworkSperical.startSet	0.327	0.041	0.370
plot.abstract.module	51.406	1.291	54.520
plot.abstract.nodes	0.286	0.006	0.293
plot.modules	38.003	1.214	39.590
plot.netbiov	0.691	0.005	0.701
plot.spiral.graph	0.372	0.006	0.383
split.mst	0.709	0.015	0.765