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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:Doscheda.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings Doscheda_1.33.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/Doscheda.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘Doscheda/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Doscheda’ version ‘1.33.0’
* 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 ‘Doscheda’ 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 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 ... OK
* checking Rd metadata ... NOTE
Invalid package aliases in Rd file 'doscheda.Rd':
  ‘doscheda-package’
* 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 ‘Doscheda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: corrPlot
> ### Title: Plot showing correlation between all channels across replicates
> ### Aliases: corrPlot corrPlot,ChemoProtSet-method corrPlot,ANY,ANY-method
> 
> ### ** Examples
> 
> 
> ex <- processedExample
> ex <- runNormalisation(ex)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached [www.humanmine.org]:
SSL connection timeout
Calls: runNormalisation ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
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:
  Backtrace:
      ▆
   1. ├─Doscheda:::normalize_data(...) at test-normal.R:8:5
   2. │ └─Doscheda:::uniprotGene(organism)
   3. │   └─httr::POST(...)
   4. │     └─httr:::request_perform(req, hu$handle$handle)
   5. │       ├─httr:::request_fetch(req$output, req$url, handle)
   6. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7. │         └─curl::curl_fetch_memory(url, handle = handle)
   8. └─curl:::raise_libcurl_error(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  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 ‘Doscheda.Rmd’ using rmarkdown

Quitting from Doscheda.Rmd:147-150 [fitModelEx]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.humanmine.org]:
SSL connection timeout
---
Backtrace:
     ▆
  1. ├─Doscheda::runNormalisation(ex)
  2. ├─Doscheda::runNormalisation(ex)
  3. │ └─Doscheda:::normalize_data(...)
  4. │   └─Doscheda:::uniprotGene(organism)
  5. │     └─httr::POST(...)
  6. │       └─httr:::request_perform(req, hu$handle$handle)
  7. │         ├─httr:::request_fetch(req$output, req$url, handle)
  8. │         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
  9. │           └─curl::curl_fetch_memory(url, handle = handle)
 10. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Doscheda.Rmd' failed with diagnostics:
Timeout was reached [www.humanmine.org]:
SSL connection timeout
--- failed re-building ‘Doscheda.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL Doscheda
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘Doscheda’ ...
** this is package ‘Doscheda’ version ‘1.33.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘getInput’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getNorm’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getFinal’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getParameters’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘getDatasets’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘boxplot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘corrPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
in method for ‘densityPlot’ with signature ‘"ChemoProtSet"’: no definition for class “ChemoProtSet”
Creating a new generic function for ‘meanSdPlot’ in package ‘Doscheda’
** 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 (Doscheda)

R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 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(Doscheda)
> 
> test_check("Doscheda")
Saving _problems/test-normal-13.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-normal.R:8:5'): normalize_data med works ───────────────────────
<curl_error_operation_timedout/curl_error/error/condition>
Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached [www.humanmine.org]:
SSL connection timeout
Backtrace:
    ▆
 1. ├─Doscheda:::normalize_data(...) at test-normal.R:8:5
 2. │ └─Doscheda:::uniprotGene(organism)
 3. │   └─httr::POST(...)
 4. │     └─httr:::request_perform(req, hu$handle$handle)
 5. │       ├─httr:::request_fetch(req$output, req$url, handle)
 6. │       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
 7. │         └─curl::curl_fetch_memory(url, handle = handle)
 8. └─curl:::raise_libcurl_error(...)

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