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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:HPiP.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings HPiP_1.17.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/HPiP.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘HPiP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HPiP’ version ‘1.17.1’
* 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 ‘HPiP’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* 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 ... NOTE
checkRd: (-1) getHPI.Rd:29: Lost braces
    29 | then the Kronecker product is the code{(pm × qn)} block matrix
       |                                       ^
* checking Rd metadata ... OK
* checking Rd cross-references ... INFO
Package unavailable to check Rd xrefs: ‘ftrCOOL’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'pred_ensembel.Rd':
pred_ensembel
  Code: function(features, gold_standard, classifier = c("avNNet",
                 "svmRadial", "ranger"), resampling.method = "cv",
                 ncross = 2, repeats = 2, verboseIter = TRUE, plots =
                 FALSE, filename = "plots.pdf")
  Docs: function(features, gold_standard, classifier = c("avNNet",
                 "svmRadial", "ranger"), resampling.method = "cv",
                 ncross = 2, repeats = 2, verboseIter = TRUE, plots =
                 TRUE, filename = "plots.pdf")
  Mismatches in argument default values:
    Name: 'plots' Code: FALSE Docs: TRUE

* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘HPiP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: enrichfindP
> ### Title: Functional Enrichment Analysis for Pathogen Interactors in the
> ###   High-Confidence Network.
> ### Aliases: enrichfindP
> 
> ### ** Examples
> 
> data('predicted_PPIs')
> #perform enrichment
> enrich.df <- enrichfindP(predicted_PPIs,
+ threshold = 0.05,
+ sources = c("GO", "KEGG"),
+ p.corrction.method = "bonferroni",
+ org = "hsapiens")
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
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
corr_plot 33.704  0.455  34.168
FSmethod  32.244  0.581  32.827
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  ERROR in test_enrich.df: 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.
  
  Test files with failing tests
  
     test_enrich.df.R 
       test_enrich.df 
  
  
  Error in BiocGenerics:::testPackage("HPiP") : 
    unit tests failed for package HPiP
  In addition: Warning messages:
  1: `repeats` has no meaning for this resampling method. 
  2: executing %dopar% sequentially: no parallel backend registered 
  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 ‘HPiP_tutorial.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/HPiP.Rcheck/vign_test/HPiP/vignettes/HPiP_tutorial_files/figure-html/unnamed-chunk-53-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/HPiP.Rcheck/vign_test/HPiP/vignettes/HPiP_tutorial_files/figure-html/unnamed-chunk-54-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/HPiP.Rcheck/vign_test/HPiP/vignettes/HPiP_tutorial_files/figure-html/unnamed-chunk-60-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/HPiP.Rcheck/vign_test/HPiP/vignettes/HPiP_tutorial_files/figure-html/unnamed-chunk-61-1.png" but not available.

Quitting from HPiP_tutorial.Rmd:1236-1242 [unnamed-chunk-64]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<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. └─HPiP::enrichfind_cpx(...)
 2.   └─base::lapply(...)
 3.     └─HPiP (local) FUN(X[[i]], ...)
 4.       └─gprofiler2::gost(...)
 5.         └─gprofiler2::gprofiler_request(url, body)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'HPiP_tutorial.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 ‘HPiP_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 3 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/HPiP.Rcheck/00check.log’
for details.