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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoRegNet.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings CoRegNet_1.41.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/CoRegNet.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'CoRegNet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CoRegNet' version '1.41.1'
* 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
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) discretizeExpressionData.Rd:73: Lost braces; missing escapes or markup?
    73 | A matrix of integers with the same number of rows and the same number of column as the input numericalExpression. Values in the output matrix are in {-1,0,1}.
       |                                                                                                                                                      ^
checkRd: (-1) hLICORN.Rd:32: Lost braces; missing escapes or markup?
    32 |   optional. Should be in exactly the same format as \code{numericalExpression} (dimensions, colnames and rownames) and should contain value only in {-1,0,1} with -1 for under-expressed, 0 for no change and 1 for over expressed. For default value see details.
       |                                                                                                                                                     ^
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'coRegnet-package.Rd':
  'coRegnet-package'
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/CoRegNet/libs/x64/CoRegNet.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
hLICORN         32.23   0.11   32.46
masterRegulator 13.24   0.02   13.26
* 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 ... 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, 5 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/CoRegNet.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL CoRegNet
###
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'CoRegNet' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c comblicorn.c -o comblicorn.o
gcc -shared -s -static-libgcc -o CoRegNet.dll tmp.def comblicorn.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-CoRegNet/00new/CoRegNet/libs/x64
** 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
Warning in fun(libname, pkgname) :
  Package 'CoRegNet' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'CoRegNet' is deprecated and will be removed from Bioconductor
  version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (CoRegNet)

R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
Warning message:
In fun(libname, pkgname) :
  Package 'CoRegNet' is deprecated and will be removed from Bioconductor
  version 3.20
> 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 -- Mon Apr 29 00:35:10 2024 
*********************************************** 
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 
Warning messages:
1: In hLICORN(ex, TFlist = LETTERS[1:5]) :
  Expression data should be in a matrix or data frame with genes in rows and samples in column.
2: In hLICORN(ex, TFlist = LETTERS[1:5], parallel = "no") :
  Expression data should be in a matrix or data frame with genes in rows and samples in column.
> 
> proc.time()
   user  system elapsed 
   5.82    0.39    6.17