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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BioNAR_1.2.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BioNAR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.2.5’
* 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 ... 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 loading without being on the library search path ... 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’ ‘storeFitInfo’
  ‘storeParInfo’
* 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                              user system elapsed
plotEntropy                 15.520  0.588  16.108
calcEntropy                 15.325  0.180  15.505
getEntropy                  14.360  0.176  14.536
getCentralityMatrix         12.694  0.155  12.849
annotateTopOntoOVG          12.641  0.080  12.721
getGraphCentralityECDF      12.618  0.072  12.690
clusteringSummary           10.893  0.012  10.906
annotateSCHanno              9.925  0.088  10.019
normModularity               8.991  0.448   9.440
buildFromSynaptomeGeneTable  8.320  0.108   8.428
buildFromSynaptomeByEntrez   8.167  0.052   8.219
calcSparsness                7.597  0.032   7.629
addEdgeAtts                  6.870  0.134   7.004
runPermDisease               6.075  0.096   6.171
FitDegree                    1.459  0.112   5.678
getRandomGraphCentrality     0.279  0.008  11.310
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘BioNAR_overview.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BioNAR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BioNAR
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘BioNAR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** testing if installed package can be loaded from final location
Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache
** testing if installed package keeps a record of temporary installation path
* DONE (BioNAR)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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.

> 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


Using 'localHub=TRUE'
  If offline, please also see BiocManager vignette section on offline use
loading from cache

Attaching package: 'BioNAR'

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

    permute

> 
> test_check("BioNAR")
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
Loading required package: synaptome.data
Loading required package: AnnotationHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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

    normalize, path, union

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: BiocFileCache
Loading required package: dbplyr
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
This graph was created by an old(er) igraph version.
  Call upgrade_graph() on it to use with the current igraph version
  For now we convert it on the fly...
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 109 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_bridgeness.R:34:5', 'test_bridgeness.R:64:5'

[ FAIL 0 | WARN 0 | SKIP 2 | PASS 109 ]
Deleting unused snapshots:
• bridgeness/entropyplot.svg
• fitdegree/powerfitplot.svg
> 
> proc.time()
   user  system elapsed 
 53.736   1.736  67.742