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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GWENA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GWENA_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/GWENA.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 ‘GWENA/DESCRIPTION’ ... OK
* this is package ‘GWENA’ version ‘1.15.0’
* 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 ‘/Users/biocbuild/bbs-3.20-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 ... 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 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 ... 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 ... 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)
> 
> multi_module <- list(mod1 = single_module,
+                      mod2 = c("TAF1C", "TARBP2", "POLH", "CETN2", "POLD1",
+                               "CANT1", "PDE4B", "DGCR8", "RAD51", "SURF1",
+                                "PNP", "ADA", "NME3", "GTF3C5", "NT5C"))
> multi_module_enriched <- bio_enrich(multi_module, custom_path)
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to biit.cs.ut.ee port 80 after 150005 ms: Couldn't connect to server
Calls: bio_enrich ... gprofiler_request -> <Anonymous> -> <Anonymous> -> fun
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:
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(28L, "Failed to connect to biit.cs.ut.ee port 80 after 150004 ms: Couldn't connect to server", 
      TRUE)`: Failed to connect to biit.cs.ut.ee port 80 after 150004 ms: Couldn't connect to server
  Backtrace:
      ▆
   1. ├─gprofiler2::gost(query, organism = gmt_symbols_id) at test-biological_integration.R:22:1
   2. │ └─gprofiler2:::gprofiler_request(url, body)
   3. │   └─RCurl::curlPerform(...)
   4. └─RCurl (local) `<fn>`(...)
  
  [ 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/GWENA.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GWENA
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘GWENA’ ...
** 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 4.4.0 Patched (2024-04-24 r86482) -- "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(GWENA)

> 
> test_check("GWENA")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 186 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-biological_integration.R:22:1'): (code run outside of `test_that()`) ──
<OPERATION_TIMEDOUT/GenericCurlError/error/condition>
Error in `function (type, msg, asError = TRUE) 
{
    if (!is.character(type)) {
        i = match(type, CURLcodeValues)
        typeName = if (is.na(i)) 
            character()
        else names(CURLcodeValues)[i]
    }
    typeName = gsub("^CURLE_", "", typeName)
    fun = (if (asError) 
        stop
    else warning)
    fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
        "GenericCurlError", "error", "condition")))
}(28L, "Failed to connect to biit.cs.ut.ee port 80 after 150004 ms: Couldn't connect to server", 
    TRUE)`: Failed to connect to biit.cs.ut.ee port 80 after 150004 ms: Couldn't connect to server
Backtrace:
    ▆
 1. ├─gprofiler2::gost(query, organism = gmt_symbols_id) at test-biological_integration.R:22:1
 2. │ └─gprofiler2:::gprofiler_request(url, body)
 3. │   └─RCurl::curlPerform(...)
 4. └─RCurl (local) `<fn>`(...)

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