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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:GWENA.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings GWENA_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.20.0’
* 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 ‘GWENA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
  Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
  Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
  Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
See ‘/home/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
 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 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 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 ... OK
* checking Rd files ... WARNING
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:91:72
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:96:77
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:98:74
prepare_Rd: bad markup (extra space?) at compare_conditions.Rd:100:69
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
 NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  build_net.Rd: adjacency.fromSimilarity
  get_fit.cor.Rd: pickSoftThreshold.fromSimilarity
  get_fit.expr.Rd: pickSoftThreshold.fromSimilarity
  plot_module.Rd: igraph.plotting
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... ERROR
Running examples in ‘GWENA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bio_enrich
> ### Title: Modules enrichment
> ### Aliases: bio_enrich
> 
> ### ** Examples
> 
> custom_path <- system.file("extdata", "h.all.v6.2.symbols.gmt",
+                            package = "GWENA", mustWork = TRUE)
> 
> single_module <- c("BIRC3", "PMAIP1", "CASP8", "JUN", "BCL2L11", "MCL1",
+                    "IL1B", "SPTAN1", "DIABLO", "BAX", "BIK", "IL1A", "BID",
+                    "CDKN1A", "GADD45A")
> single_module_enriched <- bio_enrich(single_module, custom_path)
Error: Request to g:Profiler failed (HTTP 504). The service may be temporarily unavailable.
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
Execution halted
* 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:
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-biological_integration.R:6:1'): (code run outside of `test_that()`) ──
  Error: Request to g:Profiler failed (HTTP 504). The service may be temporarily unavailable.
  If the issue persists, please contact biit.support@ut.ee with a reproducible example.
  Backtrace:
      ▆
   1. └─gprofiler2::gost(query) at test-biological_integration.R:6:1
   2.   └─gprofiler2::gprofiler_request(url, body)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘GWENA_guide.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/vign_test/GWENA/vignettes/GWENA_guide_files/figure-html/bipartite_graph_merge-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/vign_test/GWENA/vignettes/GWENA_guide_files/figure-html/plot_modules_gene_distribution-1.png" but not available.

Quitting from GWENA_guide.Rmd:282-285 [modules_enrichment]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Request to g:Profiler failed (HTTP 504). The service may be temporarily unavailable.
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
---
Backtrace:
    ▆
 1. └─GWENA::bio_enrich(modules$modules)
 2.   └─gprofiler2::gost(query = module, ...)
 3.     └─gprofiler2::gprofiler_request(url, body)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GWENA_guide.Rmd' failed with diagnostics:
Request to g:Profiler failed (HTTP 504). The service may be temporarily unavailable.
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
--- failed re-building ‘GWENA_guide.Rmd’

SUMMARY: processing the following file failed:
  ‘GWENA_guide.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/GWENA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL GWENA
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘GWENA’ ...
** this is package ‘GWENA’ version ‘1.20.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: bad markup (extra space?) at compare_conditions.Rd:91:72
Warning: bad markup (extra space?) at compare_conditions.Rd:96:77
Warning: bad markup (extra space?) at compare_conditions.Rd:98:74
Warning: bad markup (extra space?) at compare_conditions.Rd:100:69
*** 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 (GWENA)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(GWENA)

> 
> test_check("GWENA")
Saving _problems/test-biological_integration-6.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biological_integration.R:6:1'): (code run outside of `test_that()`) ──
Error: Request to g:Profiler failed (HTTP 504). The service may be temporarily unavailable.
If the issue persists, please contact biit.support@ut.ee with a reproducible example.
Backtrace:
    ▆
 1. └─gprofiler2::gost(query) at test-biological_integration.R:6:1
 2.   └─gprofiler2::gprofiler_request(url, body)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]
Error:
! Test failures.
Execution halted