##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FELLA.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FELLA_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.26.0’
* 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 ‘FELLA’ 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 ... NOTE
buildGraphFromKEGGREST: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'dot-params.Rd':
  ‘databaseDir’ ‘internalDir’ ‘object’ ‘data’ ‘type’ ‘level’ ‘method’
  ‘methods’ ‘approx’ ‘loadMatrix’ ‘threshold’
  ‘thresholdConnectedComponent’ ‘plimit’ ‘nlimit’ ‘niter’ ‘layout’
  ‘graph’ ‘GOterm’ ‘GONamesAsLabels’ ‘LabelLengthAtPlot’
  ‘godata.options’ ‘mart.options’ ‘p.adjust’ ‘dampingFactor’ ‘t.df’
  ‘compounds’ ‘compoundsBackground’ ‘NamesAsLabels’ ‘capPscores’

Documented arguments not in \usage in Rd file 'infere.con2ec.Rd':
  ‘gene2enyzme’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
data-funs 6.192  0.179   6.372
* 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:
   11.         └─FELLA (local) .fun(piece, ...)
   12.           └─KEGGREST::keggLink(row[1], row[2])
   13.             └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
   14.               └─httr::stop_for_status(response)
  ── Error ('test-databaseCreation.R:31:5'): The graph can be parsed from KEGGREST ──
  Error in `eval(code, test_env)`: object 'g.full' not found
  Backtrace:
      ▆
   1. └─testthat::expect_is(g.full, "igraph") at test-databaseCreation.R:31:5
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 2 | WARN 9 | SKIP 0 | PASS 166 ]
  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 ‘musmusculus.Rmd’ using rmarkdown

Quitting from musmusculus.Rmd:41-67 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getUrl()`:
! Bad Request (HTTP 400).
---
Backtrace:
    x
 1. \-FELLA::buildGraphFromKEGGREST(...)
 2.   \-plyr::alply(...)
 3.     \-plyr::llply(...)
 4.       +-plyr:::loop_apply(n, do.ply)
 5.       \-plyr (local) `<fn>`(1L)
 6.         \-FELLA (local) .fun(piece, ...)
 7.           \-KEGGREST::keggLink(row[1], row[2])
 8.             \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 9.               \-httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘quickstart.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/vign_test/FELLA/vignettes/quickstart_files/figure-html/unnamed-chunk-14-1.png" but not available.
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘zebrafish.Rmd’ using rmarkdown

Quitting from zebrafish.Rmd:50-74 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getUrl()`:
! Bad Request (HTTP 400).
---
Backtrace:
    x
 1. \-FELLA::buildGraphFromKEGGREST(organism = "dre", filter.path = c("01100"))
 2.   \-plyr::alply(...)
 3.     \-plyr::llply(...)
 4.       +-plyr:::loop_apply(n, do.ply)
 5.       \-plyr (local) `<fn>`(1L)
 6.         \-FELLA (local) .fun(piece, ...)
 7.           \-KEGGREST::keggLink(row[1], row[2])
 8.             \-KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 9.               \-httr::stop_for_status(response)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘FELLA.Rnw’ using Sweave
Building through KEGGREST...
Available gene annotations: ncbi-geneid, ncbi-proteinid. Using ncbi-geneid

Error: processing vignette 'FELLA.Rnw' failed with diagnostics:
 chunk 2 (label = 01_graph) 
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) : 
  Bad Request (HTTP 400).

--- failed re-building ‘FELLA.Rnw’

SUMMARY: processing the following files failed:
  ‘musmusculus.Rmd’ ‘zebrafish.Rmd’ ‘FELLA.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/FELLA.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FELLA
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘FELLA’ ...
** using staged installation
** R
** data
** inst
** 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 (FELLA)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
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(FELLA)
> 
> test_check("FELLA")

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[ FAIL 2 | WARN 9 | SKIP 0 | PASS 166 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-databaseCreation.R:27:5'): The graph can be parsed from KEGGREST ──
`{ ... }` threw an error.
Message: Bad Request (HTTP 400).
Class:   http_400/http_error/error/condition
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test-databaseCreation.R:27:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─FELLA::buildGraphFromKEGGREST(organism = "gla") at test-databaseCreation.R:28:9
  7.   └─plyr::alply(...)
  8.     └─plyr::llply(...)
  9.       ├─plyr:::loop_apply(n, do.ply)
 10.       └─plyr (local) `<fn>`(1L)
 11.         └─FELLA (local) .fun(piece, ...)
 12.           └─KEGGREST::keggLink(row[1], row[2])
 13.             └─KEGGREST:::.getUrl(url, .listParser, nameColumn = 1, valueColumn = 2)
 14.               └─httr::stop_for_status(response)
── Error ('test-databaseCreation.R:31:5'): The graph can be parsed from KEGGREST ──
Error in `eval(code, test_env)`: object 'g.full' not found
Backtrace:
    ▆
 1. └─testthat::expect_is(g.full, "igraph") at test-databaseCreation.R:31:5
 2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
 3.     └─rlang::eval_bare(expr, quo_get_env(quo))

[ FAIL 2 | WARN 9 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted