Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLM[N]OPQRSTUVWXYZ

This page was generated on 2022-04-13 12:05:41 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for netbiov on nebbiolo2


To the developers/maintainers of the netbiov package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netbiov.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1281/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
netbiov 1.28.0  (landing page)
Shailesh tripathi
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/netbiov
git_branch: RELEASE_3_14
git_last_commit: 27d072e
git_last_commit_date: 2021-10-26 12:14:46 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: netbiov
Version: 1.28.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netbiov.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netbiov_1.28.0.tar.gz
StartedAt: 2022-04-12 08:27:47 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:29:47 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 120.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: netbiov.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:netbiov.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings netbiov_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/netbiov.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.28.0’
* 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 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 (user + system) or elapsed time > 5s
                       user system elapsed
plot.abstract.module 23.850  0.387  24.239
level.plot           22.769  0.263  23.034
plot.modules         18.489  0.012  18.501
mst.plot              8.277  0.087   8.366
* 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 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/netbiov.Rcheck/00check.log’
for details.



Installation output

netbiov.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL netbiov
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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)

Tests output

netbiov.Rcheck/tests/runTests.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Tue Apr 12 08:29:43 2022 
*********************************************** 
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 12 08:29:43 2022 
*********************************************** 
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 
  8.374   0.456   8.816 

Example timings

netbiov.Rcheck/netbiov-Ex.timings

nameusersystemelapsed
PPI_Athalina0.0130.0000.013
level.plot22.769 0.26323.034
mst.plot8.2770.0878.366
mst.plot.mod3.4440.0323.476
plot.NetworkSperical0.5030.0010.503
plot.NetworkSperical.startSet0.1210.0000.120
plot.abstract.module23.850 0.38724.239
plot.abstract.nodes0.1830.0080.190
plot.modules18.489 0.01218.501
plot.netbiov0.4370.0000.437
plot.spiral.graph0.2820.0040.287
split.mst0.560.000.56