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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbKegg_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbKegg.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 ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ version ‘1.12.0’
* 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 ‘biodbKegg’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 whether startup messages can be suppressed ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
KeggEnzymeConn   13.317  0.625 114.959
KeggPathwayConn   5.538  0.253  50.706
KeggCompoundConn  2.104  0.123  10.416
* 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:
  ── Failure ('test_700_reaction.R:16:1'): We can search for an entry by name. ───
  id %in% ids is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  While searching for entry R00105 by name "ATP:NADH 2'-phosphotransferase".
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
   3.   └─testthat::expect_true(id %in% ids, msg)
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 1469 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbKegg.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbKegg
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘biodbKegg’ ...
** using staged installation
** R
** 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
Warning in fun(libname, pkgname) :
  Package 'biodbKegg' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbKegg' is deprecated and will be removed from Bioconductor
  version 3.21
** testing if installed package keeps a record of temporary installation path
* DONE (biodbKegg)

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.

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbKegg' is deprecated and will be removed from Bioconductor
  version 3.21
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png?17413128691255063'
downloaded 158 KB

[ FAIL 12 | WARN 0 | SKIP 0 | PASS 1469 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_compound.R:184:1'): ppm tolerance works in annotateMzValues() ──
c("mz", id.col) not identical to colnames(ret).
Lengths differ: 2 is not 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure ('test_300_genes.R:32:1'): We can search for an entry by searchable field ──
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_300_genes.R:32:1'): We can search for an entry by searchable field ──
c(`mmu%3A14635` = "mmu:14635") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_400_module.R:16:1'): We can search for an entry by searchable field ──
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_400_module.R:16:1'): We can search for an entry by searchable field ──
c(M00009 = "M00009") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_400_module.R:16:1'): We can search for an entry by name. ─────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry M00009 by name "Citrate cycle (TCA cycle, Krebs cycle)".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_400_module.R:16:1'): We can search for an entry by name. ─────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry M00009 by name "Citrate cycle (TCA cycle, Krebs cycle)".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_600_pathway.R:103:1'): extractPathwayMapShapes() works correctly. ──
`shapes` has length 2, not length 1.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg (local) `<fn>`(conn = `<KggPthwC>`)
 3.   └─testthat::expect_length(shapes, items[[i]]) at test_600_pathway.R:68:9
── Failure ('test_700_reaction.R:16:1'): We can search for an entry by searchable field ──
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_700_reaction.R:16:1'): We can search for an entry by searchable field ──
c(R00105 = "R00105") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_700_reaction.R:16:1'): We can search for an entry by name. ───
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry R00105 by name "ATP:NADH 2'-phosphotransferase".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_700_reaction.R:16:1'): We can search for an entry by name. ───
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry R00105 by name "ATP:NADH 2'-phosphotransferase".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)

[ FAIL 12 | WARN 0 | SKIP 0 | PASS 1469 ]
Error: Test failures
Execution halted