R version 4.4.1 (2024-06-14) -- "Race for Your Life"
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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbKegg)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodbKegg")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 1831 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_long_100_compound.R:16:1'): We can search for an entry by searchable field ──
c(C00133 = "C00133") %in% "C00041" is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_long_100_compound.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 C00133 by name "D-Alanine".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_long_100_compound.R:16:1'): We can search for a compound ─────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by name "D-Alanine".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_long_100_compound.R:16:1'): ppm tolerance works in annotateMzValues() ──
any(is.na(ret[[id.col]])) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(any(is.na(ret[[id.col]])))

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 1831 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbKegg_1.10.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbKegg.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’
* checking for file ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ version ‘1.10.2’
* 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 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 ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in ‘longtests’ ... OK
* checking tests in ‘longtests’ ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘longtests/testthat.R’ failed.
Last 13 lines of output:
   3.   └─testthat::expect_true(id %in% ids, msg)
  ── Failure ('test_long_100_compound.R:16:1'): ppm tolerance works in annotateMzValues() ──
  any(is.na(ret[[id.col]])) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(any(is.na(ret[[id.col]])))
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 1831 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc-longtests/meat/biodbKegg.Rcheck/00check.log’
for details.

* 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbKegg)