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CHECK report for netbiov on malbec1

This page was generated on 2018-04-12 13:12:26 -0400 (Thu, 12 Apr 2018).

Package 935/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbiov 1.12.0
Shailesh tripathi
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/netbiov
Branch: RELEASE_3_6
Last Commit: 0e4040c
Last Changed Date: 2017-10-30 12:40:19 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: netbiov
Version: 1.12.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings netbiov_1.12.0.tar.gz
StartedAt: 2018-04-12 01:27:28 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:30:25 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 177.0 seconds
RetCode: 0
Status:  OK 
CheckDir: netbiov.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings netbiov_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/netbiov.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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 ... NOTE
  installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
* 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 loading without being on the library search path ... 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’
.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 installed files from ‘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           59.460  0.320  59.885
plot.abstract.module 33.060  0.048  33.131
plot.modules         26.772  0.036  26.845
mst.plot             10.244  0.052  10.300
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/netbiov.Rcheck/00check.log’
for details.



Installation output

netbiov.Rcheck/00install.out

* installing *source* package ‘netbiov’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (netbiov)

Tests output

netbiov.Rcheck/tests/runTests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Thu Apr 12 01:30:22 2018 
*********************************************** 
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 -- Thu Apr 12 01:30:22 2018 
*********************************************** 
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 
 10.712   0.160  10.885 

Example timings

netbiov.Rcheck/netbiov-Ex.timings

nameusersystemelapsed
PPI_Athalina0.0120.0040.016
level.plot59.460 0.32059.885
mst.plot10.244 0.05210.300
mst.plot.mod4.2160.0204.240
plot.NetworkSperical0.9680.0000.969
plot.NetworkSperical.startSet0.5440.0200.564
plot.abstract.module33.060 0.04833.131
plot.abstract.nodes0.3720.0000.369
plot.modules26.772 0.03626.845
plot.netbiov0.4560.0000.460
plot.spiral.graph0.3600.0120.372
split.mst0.5920.0000.593