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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netOmics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netOmics_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/netOmics.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netOmics/DESCRIPTION’ ... OK
* this is package ‘netOmics’ version ‘1.4.0’
* 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 ... 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 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 0.23  0.021  17.059
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   11.   └─vctrs::vec_default_cast(...)
   12.     ├─base::withRestarts(...)
   13.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
   14.     │   └─base (local) doWithOneRestart(return(expr), restart)
   15.     └─vctrs::stop_incompatible_cast(...)
   16.       └─vctrs::stop_incompatible_type(...)
   17.         └─vctrs:::stop_incompatible(...)
   18.           └─vctrs:::stop_vctrs(...)
   19.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
  ── Failure ('test-combine_layers.R:53:5'): combine_layers works ────────────────
  `combine_layers(graph1 = graph1, interaction.df = interaction.df2)` did not produce any warnings.
  
  [ FAIL 2 | WARN 1 | SKIP 0 | PASS 137 ]
  Error: Test failures
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/netOmics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netOmics
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 2 | WARN 1 | SKIP 0 | PASS 137 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-RWR.R:119:5'): rwr_find_closest_type works ─────────────────────
<vctrs_error_cast/vctrs_error_incompatible_type/vctrs_error_incompatible/vctrs_error/rlang_error/error/condition>
Error in `tidyr::pivot_longer(rwr.res.filtered, names_to = "attribute", 
    values_to = "value", -c(NodeNames, Score, SeedName), values_ptypes = list(value = character()))`: Can't convert `type` <logical> to <character>.
Backtrace:
     ▆
  1. ├─testthat::expect_is(...) at test-RWR.R:119:4
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─netOmics::rwr_find_closest_type(X = rwr_res, seed = "Z")
  5. │ └─netOmics:::.rwr_find_closest(...)
  6. │   ├─tidyr::pivot_longer(...)
  7. │   └─tidyr:::pivot_longer.data.frame(...)
  8. │     └─tidyr::pivot_longer_spec(...)
  9. │       └─vctrs::vec_cast_common(!!!val_cols, .to = val_type, .call = error_call)
 10. └─vctrs (local) `<fn>`()
 11.   └─vctrs::vec_default_cast(...)
 12.     ├─base::withRestarts(...)
 13.     │ └─base (local) withOneRestart(expr, restarts[[1L]])
 14.     │   └─base (local) doWithOneRestart(return(expr), restart)
 15.     └─vctrs::stop_incompatible_cast(...)
 16.       └─vctrs::stop_incompatible_type(...)
 17.         └─vctrs:::stop_incompatible(...)
 18.           └─vctrs:::stop_vctrs(...)
 19.             └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Failure ('test-combine_layers.R:53:5'): combine_layers works ────────────────
`combine_layers(graph1 = graph1, interaction.df = interaction.df2)` did not produce any warnings.

[ FAIL 2 | WARN 1 | SKIP 0 | PASS 137 ]
Error: Test failures
Execution halted