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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:famat.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings famat_1.19.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/famat.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘famat/DESCRIPTION’ ... OK
* this is package ‘famat’ version ‘1.19.0’
* 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 ‘famat’ 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘BiasedUrn’ ‘mgcv’ ‘stats’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Getenvir: no visible binding for global variable ‘MPINetData’
Undefined global functions or variables:
  MPINetData
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘famat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interactions
> ### Title: Interactions between genes and metabolites
> ### Aliases: interactions
> 
> ### ** Examples
> 
>     ## load example data
>     data(listk)
>     data(listr)
>     data(listw)
> 
>     interactions_result=interactions(listk,listr,listw)
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Bad Request (HTTP 400).
Calls: interactions ... <Anonymous> -> lapply -> FUN -> .getUrl -> stop_for_status
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
compl_data 77.87  3.187  85.468
* 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:
  ── Error ('test-interactions.R:6:1'): (code run outside of `test_that()`) ──────
  <http_400/http_error/error/condition>
  Error in `.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)`: Bad Request (HTTP 400).
  Backtrace:
      ▆
   1. └─famat::interactions(listk, listr, listw) at test-interactions.R:6:1
   2.   └─KEGGREST::keggConv("chebi", "compound")
   3.     └─base::lapply(groups, .keggConv, target = target)
   4.       └─KEGGREST (local) FUN(X[[i]], ...)
   5.         └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
   6.           └─httr::stop_for_status(response)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]
  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 ‘famat.Rmd’ using rmarkdown

Quitting from famat.Rmd:78-84 [interactions]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getUrl()`:
! Bad Request (HTTP 400).
---
Backtrace:
    ▆
 1. └─famat::interactions(listk, listr, listw)
 2.   └─KEGGREST::keggConv("chebi", "compound")
 3.     └─base::lapply(groups, .keggConv, target = target)
 4.       └─KEGGREST (local) FUN(X[[i]], ...)
 5.         └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 6.           └─httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'famat.Rmd' failed with diagnostics:
Bad Request (HTTP 400).
--- failed re-building ‘famat.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL famat
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘famat’ ...
** this is package ‘famat’ version ‘1.19.0’
** using staged installation
** R
** data
** 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 (famat)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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(famat)

> 
> test_check("famat")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 1 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-compl_data.R:6:1'): (code run outside of `test_that()`) ────────
<http_400/http_error/error/condition>
Error in `.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)`: Bad Request (HTTP 400).
Backtrace:
    ▆
 1. └─famat::interactions(listk, listr, listw) at test-compl_data.R:6:1
 2.   └─KEGGREST::keggConv("chebi", "compound")
 3.     └─base::lapply(groups, .keggConv, target = target)
 4.       └─KEGGREST (local) FUN(X[[i]], ...)
 5.         └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 6.           └─httr::stop_for_status(response)
── Error ('test-interactions.R:6:1'): (code run outside of `test_that()`) ──────
<http_400/http_error/error/condition>
Error in `.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)`: Bad Request (HTTP 400).
Backtrace:
    ▆
 1. └─famat::interactions(listk, listr, listw) at test-interactions.R:6:1
 2.   └─KEGGREST::keggConv("chebi", "compound")
 3.     └─base::lapply(groups, .keggConv, target = target)
 4.       └─KEGGREST (local) FUN(X[[i]], ...)
 5.         └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 6.           └─httr::stop_for_status(response)

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