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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:netOmics.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings netOmics_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/netOmics.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘netOmics/DESCRIPTION’ ... OK
* this is package ‘netOmics’ version ‘1.8.0’
* 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 ‘netOmics’ 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 ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.interaction_from_dataframe: no visible binding for global variable ‘.’
.rwr_find_closest: no visible binding for global variable ‘SeedName’
.rwr_find_closest: no visible binding for global variable ‘NodeNames’
.rwr_find_closest: no visible binding for global variable ‘Score’
.rwr_find_closest: no visible binding for global variable ‘attribute’
.rwr_find_closest: no visible binding for global variable ‘value’
combine_layers: no visible binding for global variable ‘.’
get_grn: no visible binding for global variable ‘.’
get_interaction_from_ORA: no visible binding for global variable
  ‘significant’
get_interaction_from_ORA: no visible binding for global variable
  ‘term_id’
get_interaction_from_ORA: no visible binding for global variable
  ‘target’
get_interaction_from_ORA: no visible binding for global variable
  ‘input’
plot_rwr_subnetwork: no visible binding for global variable ‘rwr’
plot_rwr_subnetwork: no visible binding for global variable ‘type’
plot_rwr_subnetwork: no visible binding for global variable ‘N’
plot_rwr_subnetwork: no visible global function definition for ‘title’
plot_rwr_subnetwork: no visible binding for global variable ‘name’
rwr_top_k_graph: no visible binding for global variable ‘SeedName’
rwr_top_k_graph: no visible binding for global variable ‘Score’
rwr_top_k_graph: no visible binding for global variable ‘NodeNames’
summary_plot_rwr_attributes: no visible binding for global variable
  ‘seed’
summary_plot_rwr_attributes: no visible binding for global variable ‘N’
summary_plot_rwr_attributes: no visible binding for global variable
  ‘type’
Undefined global functions or variables:
  . N NodeNames Score SeedName attribute input name rwr seed
  significant target term_id title type value
Consider adding
  importFrom("graphics", "title")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
get_interaction_from_ORA 0.274  0.008  10.828
* 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 ...
  ‘netOmics.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-3.18-bioc/meat/netOmics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL netOmics
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘netOmics’ ...
** using staged installation
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (netOmics)

R version 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
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(netOmics)

> 
> test_check("netOmics")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 140 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 140 ]
> 
> proc.time()
   user  system elapsed 
 19.901   1.102  48.936