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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.6.0’
* package encoding: UTF-8
* 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 ‘BioNAR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   6.1Mb
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: ‘Rdpack’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addNoise’ ‘gofs’ ‘highlightRate’ ‘plotSigmoid’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterORA : forafun: no visible binding for global variable ‘pathway’
clusterORA : forafun: no visible binding for global variable ‘size’
clusterORA : forafun: no visible binding for global variable ‘overlap’
clusterORA : forafun: no visible binding for global variable ‘pval’
clusterORA : forafun: no visible binding for global variable ‘padj’
clusterORA : forafun: no visible binding for global variable
  ‘overlapGenes’
clusterORA : forafun: no visible binding for global variable ‘FL’
clusterORA : forafun: no visible binding for global variable ‘N’
clusterORA : forafun: no visible binding for global variable ‘Fn’
clusterORA : forafun: no visible binding for global variable ‘Cn’
clusterORA : forafun: no visible binding for global variable ‘Mu’
clusterORA : forafun: no visible binding for global variable ‘OR’
clusterORA : forafun: no visible binding for global variable ‘CIw’
clusterORA : forafun: no visible binding for global variable ‘Fe’
clusterORA : forafun: no visible binding for global variable ‘Fc’
clusterORA : forafun: no visible binding for global variable ‘palt’
plotSigmoid: no visible binding for global variable ‘yiR1’
plotSigmoid: no visible binding for global variable ‘yiR2’
plotSigmoid: no visible binding for global variable ‘yiR3’
plotSigmoid: no visible binding for global variable ‘yiR4’
plotSigmoid: no visible binding for global variable ‘yiR5’
Undefined global functions or variables:
  CIw Cn FL Fc Fe Fn Mu N OR overlap overlapGenes padj palt pathway
  pval size yiR1 yiR2 yiR3 yiR4 yiR5
* checking Rd files ... NOTE
checkRd: (-1) FitDegree.Rd:34: Lost braces
    34 | \item{legpos}{position of the legend @seealso{legend}}
       |                                              ^
checkRd: (-1) calcEntropy.Rd:52: Lost braces; missing escapes or markup?
    52 | Other {Entropy Functions}: 
       |       ^
checkRd: (-1) getEntropy.Rd:66: Lost braces; missing escapes or markup?
    66 | Other {Entropy Functions}: 
       |       ^
checkRd: (-1) getEntropyRate.Rd:41: Lost braces; missing escapes or markup?
    41 | Other {Entropy Functions}: 
       |       ^
checkRd: (-1) getRobustness.Rd:49: Lost braces; missing escapes or markup?
    49 | Other {Robustness functions}: 
       |       ^
checkRd: (-1) makeConsensusMatrix.Rd:69: Lost braces; missing escapes or markup?
    69 | Other {Robustness functions}: 
       |       ^
checkRd: (-1) plotEntropy.Rd:57: Lost braces; missing escapes or markup?
    57 | Other {Entropy Functions}: 
       |       ^
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
clusteringSummary        21.243  0.119  23.318
plotEntropy              18.903  0.606  21.278
addEdgeAtts              17.697  1.783  21.128
calcEntropy              18.664  0.593  20.921
getEntropy               17.700  0.597  20.225
getGraphCentralityECDF   15.749  0.463  18.091
annotateTopOntoOVG       15.553  0.526  17.518
getCentralityMatrix      15.534  0.506  17.511
runPermDisease           10.876  0.145  11.872
annotateSCHanno          10.146  0.445  11.604
annotateGOont             8.770  0.938  10.699
normModularity            8.711  0.421   9.932
calcSparsness             8.170  0.415   9.310
annotateGoBP              6.939  0.407   7.940
calcAllClustering         6.689  0.055   7.074
annotateGoMF              5.597  0.281   6.343
annotateGoCC              5.092  0.267   5.831
FitDegree                 2.258  0.068  13.614
getRandomGraphCentrality  1.103  0.035  28.609
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/BioNAR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNAR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BioNAR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (BioNAR)

R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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.

> library(testthat)
> library(BioNAR)
Loading required package: igraph

Attaching package: 'igraph'

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

    compare

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

    decompose, spectrum

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

    union

Loading required package: poweRlaw
Loading required package: latex2exp
Loading required package: RSpectra
Loading required package: Rdpack



Attaching package: 'BioNAR'

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

    permute

> 
> test_check("BioNAR")
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 129 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_bridgeness.R:38:5', 'test_bridgeness.R:81:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 129 ]
> 
> proc.time()
   user  system elapsed 
 70.120   3.358 105.408