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CHECK report for CoRegNet on tokay2

This page was generated on 2020-10-17 11:56:22 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CoRegNet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 375/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoRegNet 1.26.0
Remy Nicolle
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CoRegNet
Branch: RELEASE_3_11
Last Commit: 66c31b2
Last Changed Date: 2020-04-27 14:44:47 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: CoRegNet
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CoRegNet_1.26.0.tar.gz
StartedAt: 2020-10-17 02:57:04 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:00:28 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 203.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: CoRegNet.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoRegNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CoRegNet_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CoRegNet.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoRegNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoRegNet' version '1.26.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/CoRegNet/libs/i386/CoRegNet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/CoRegNet/libs/x64/CoRegNet.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
hLICORN         24.95   0.03   24.99
masterRegulator 10.13   0.00   10.12
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
hLICORN         27.87   0.05   27.92
masterRegulator 10.94   0.00   10.94
* checking for unstated dependencies in 'tests' ... WARNING
'::' or ':::' import not declared from: 'BiocGenerics'
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/CoRegNet.Rcheck/00check.log'
for details.

Installation output

CoRegNet.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/CoRegNet_1.26.0.tar.gz && rm -rf CoRegNet.buildbin-libdir && mkdir CoRegNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoRegNet.buildbin-libdir CoRegNet_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL CoRegNet_1.26.0.zip && rm CoRegNet_1.26.0.tar.gz CoRegNet_1.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4984k  100 4984k    0     0  47.6M      0 --:--:-- --:--:-- --:--:-- 50.7M

install for i386

* installing *source* package 'CoRegNet' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c comblicorn.c -o comblicorn.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CoRegNet.dll tmp.def comblicorn.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CoRegNet.buildbin-libdir/00LOCK-CoRegNet/00new/CoRegNet/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CoRegNet'
    finding HTML links ... done
    CoRegNet-class                          html  
    HumanDataExamples                       html  
    HumanTF                                 html  
    addEvidences                            html  
    coRegnet-package                        html  
    coregnet                                html  
    coregulators                            html  
    discretizeExpressionData                html  
    display                                 html  
    hLICORN                                 html  
    masterRegulator                         html  
    refine                                  html  
    regulatorInfluence                      html  
    regulators                              html  
    summary                                 html  
** 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

install for x64

* installing *source* package 'CoRegNet' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c comblicorn.c -o comblicorn.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CoRegNet.dll tmp.def comblicorn.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/CoRegNet.buildbin-libdir/CoRegNet/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoRegNet' as CoRegNet_1.26.0.zip
* DONE (CoRegNet)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'CoRegNet' successfully unpacked and MD5 sums checked

Tests output

CoRegNet.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 -- Sat Oct 17 03:00:11 2020 
*********************************************** 
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 
   4.82    0.23    5.48

CoRegNet.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Sat Oct 17 03:00:17 2020 
*********************************************** 
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 
   4.98    0.21    5.18

Example timings

CoRegNet.Rcheck/examples_i386/CoRegNet-Ex.timings

nameusersystemelapsed
HumanDataExamples0.030.020.05
HumanTF0.010.010.03
addEvidences0.200.000.21
coregnet0.060.000.06
coregulators0.080.000.08
discretizeExpressionData0.050.020.06
display0.230.000.23
hLICORN24.95 0.0324.99
masterRegulator10.13 0.0010.12
refine0.280.000.28
regulatorInfluence0.170.000.18
regulators0.020.020.03
summary0.010.000.01

CoRegNet.Rcheck/examples_x64/CoRegNet-Ex.timings

nameusersystemelapsed
HumanDataExamples0.030.000.03
HumanTF0.010.000.02
addEvidences0.140.000.14
coregnet0.040.000.03
coregulators0.070.000.08
discretizeExpressionData0.050.000.04
display0.190.000.19
hLICORN27.87 0.0527.92
masterRegulator10.94 0.0010.94
refine0.280.000.28
regulatorInfluence0.170.000.17
regulators0.030.000.03
summary0.020.000.02