Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:38 -0400 (Fri, 15 Oct 2021).

CHECK results for CoRegNet on nebbiolo1

To the developers/maintainers of the CoRegNet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoRegNet.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 392/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoRegNet 1.30.0  (landing page)
Remy Nicolle
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/CoRegNet
git_branch: RELEASE_3_13
git_last_commit: 340f25d
git_last_commit_date: 2021-05-19 12:09:00 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: CoRegNet
Version: 1.30.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CoRegNet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CoRegNet_1.30.0.tar.gz
StartedAt: 2021-10-14 09:23:41 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:25:10 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 88.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CoRegNet.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CoRegNet.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CoRegNet_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CoRegNet.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoRegNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CoRegNet’ version ‘1.30.0’
* 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 ‘CoRegNet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘gplots’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.descriptionUpdate: no visible global function definition for ‘vcount’
.descriptionUpdate: no visible global function definition for
  ‘fisher.test’
.distfun: no visible global function definition for ‘as.dist’
.distfun: no visible global function definition for ‘cor’
.fitGRN : <anonymous>: no visible global function definition for ‘lm’
.fitGRN : <anonymous>: no visible global function definition for ‘coef’
.fitGRN: no visible global function definition for ‘cor’
.fitGRN: no visible global function definition for ‘lm’
.fitGRN: no visible global function definition for ‘coef’
.hclustfun: no visible global function definition for ‘hclust’
.heatplot: no visible global function definition for ‘rainbow’
.heatplot : distf: no visible global function definition for ‘as.dist’
.heatplot : distf: no visible global function definition for ‘cor’
.heatplot : hclustf: no visible global function definition for ‘hclust’
.heatplot: no visible global function definition for ‘colorRampPalette’
.heatplot: no visible global function definition for ‘heatmap.2’
.heatplot: no visible global function definition for ‘quantile’
.tfPlot: no visible global function definition for ‘colorRampPalette’
.tfPlot: no visible global function definition for ‘rainbow’
.tfPlot: no visible global function definition for ‘par’
.tfPlot: no visible global function definition for ‘mtext’
.tfPlot: no visible global function definition for ‘quantile’
.traits : <anonymous>: no visible global function definition for
  ‘lines’
.traits: no visible global function definition for ‘abline’
automaticParameters: no visible global function definition for
  ‘quantile’
automaticParameters : <anonymous>: no visible global function
  definition for ‘pnorm’
automaticParameters: no visible global function definition for ‘abline’
automaticParameters: no visible global function definition for ‘sd’
coregnet : <anonymous>: no visible global function definition for ‘cor’
coregnet: no visible global function definition for ‘cor’
directedNetworkEnrichment: no visible global function definition for
  ‘fisher.test’
discretizeExpressionData: no visible global function definition for
  ‘sd’
fishersMethod: no visible global function definition for ‘pchisq’
legendPlot: no visible global function definition for ‘par’
legendPlot: no visible global function definition for
  ‘colorRampPalette’
legendPlot: no visible global function definition for ‘axis’
legendPlot: no visible global function definition for ‘rainbow’
list.enriched: no visible global function definition for ‘wilcox.test’
networkLegendPlot: no visible global function definition for ‘par’
networkLegendPlot: no visible global function definition for ‘symbols’
networkLegendPlot: no visible global function definition for ‘text’
networkLegendPlot: no visible global function definition for ‘rainbow’
networkLegendPlot: no visible global function definition for ‘segments’
networkLegendPlot: no visible global function definition for ‘arrows’
reactiveAdjacencyMatrix : <anonymous>: no visible global function
  definition for ‘rainbow’
set.overlap: no visible global function definition for ‘fisher.test’
undirectedNetworkEnrichment: no visible global function definition for
  ‘fisher.test’
updateData : <anonymous> : <anonymous>: no visible global function
  definition for ‘t.test’
activators,coregnet: no visible global function definition for
  ‘na.omit’
coregulators,coregnet: no visible global function definition for
  ‘p.adjust’
coregulators,coregnet : <anonymous>: no visible global function
  definition for ‘fisher.test’
refine,coregnet: no visible global function definition for ‘glm’
refine,coregnet: no visible global function definition for ‘abline’
regulatorInfluence,coregnet : <anonymous> : <anonymous>: no visible
  global function definition for ‘t.test’
regulators,coregnet: no visible global function definition for
  ‘na.omit’
repressors,coregnet: no visible global function definition for
  ‘na.omit’
targets,coregnet: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  abline arrows as.dist axis coef colorRampPalette cor fisher.test glm
  hclust heatmap.2 lines lm mtext na.omit p.adjust par pchisq pnorm
  quantile rainbow sd segments symbols t.test text vcount wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "abline", "arrows", "axis", "lines", "mtext",
             "par", "segments", "symbols", "text")
  importFrom("stats", "as.dist", "coef", "cor", "fisher.test", "glm",
             "hclust", "lm", "na.omit", "p.adjust", "pchisq", "pnorm",
             "quantile", "sd", "t.test", "wilcox.test")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
hLICORN         34.116  1.978  18.107
masterRegulator 14.140  0.595   7.409
* checking for unstated dependencies in ‘tests’ ... WARNING
'::' or ':::' import not declared from: ‘BiocGenerics’
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/CoRegNet.Rcheck/00check.log’
for details.



Installation output

CoRegNet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CoRegNet
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘CoRegNet’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c comblicorn.c -o comblicorn.o
gcc -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o CoRegNet.so comblicorn.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-CoRegNet/00new/CoRegNet/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoRegNet)

Tests output

CoRegNet.Rcheck/tests/runTests.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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(CoRegNet) || stop("unable to load CoRegNet package")
Loading required package: CoRegNet
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

Loading required package: shiny
Loading required package: arules
Loading required package: Matrix

Attaching package: 'arules'

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

    abbreviate, write

[1] TRUE
> BiocGenerics:::testPackage('CoRegNet')

Attaching package: 'RUnit'

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

    inspect

evidence1 was integrated into the network.
[1] "coregevidence1"
[1] "coregevidence1 was integrated into the network."
evidence1 was integrated into the network.
[1] "coregevidence1"
[1] "coregevidence1 was integrated into the network."


RUNIT TEST PROTOCOL -- Thu Oct 14 09:25:07 2021 
*********************************************** 
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CoRegNet RUnit Tests - 8 test functions, 0 errors, 0 failures
Number of test functions: 8 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  5.172   1.993   5.349 

Example timings

CoRegNet.Rcheck/CoRegNet-Ex.timings

nameusersystemelapsed
HumanDataExamples0.020.000.02
HumanTF0.0030.0020.005
addEvidences0.2110.2660.286
coregnet0.0510.1210.096
coregulators0.0630.1760.131
discretizeExpressionData0.0430.0040.046
display0.0510.1430.226
hLICORN34.116 1.97818.107
masterRegulator14.140 0.595 7.409
refine0.3150.6050.519
regulatorInfluence0.0450.1620.204
regulators0.1910.2170.093
summary0.0220.1150.077