Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-01 12:07:50 -0400 (Wed, 01 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for biodbKegg on merida1


To the developers/maintainers of the biodbKegg package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbKegg.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 180/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbKegg 1.2.0  (landing page)
Pierrick Roger
Snapshot Date: 2022-05-31 13:55:12 -0400 (Tue, 31 May 2022)
git_url: https://git.bioconductor.org/packages/biodbKegg
git_branch: RELEASE_3_15
git_last_commit: 3167f7e
git_last_commit_date: 2022-04-26 12:19:28 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: biodbKegg
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.2.0.tar.gz
StartedAt: 2022-05-31 23:33:57 -0400 (Tue, 31 May 2022)
EndedAt: 2022-05-31 23:47:38 -0400 (Tue, 31 May 2022)
EllapsedTime: 821.5 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbKegg.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbKegg_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/biodbKegg.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ version ‘1.2.0’
* 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 R 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 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   8.980  0.290  10.885
KeggCompoundConn 6.545  0.691  11.523
* 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 (???): The peak table is correct. ───────────────────────────────────
  any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  One of the entries is NULL.
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
   3.   └─testthat::expect_false(...)
  
  [ FAIL 137 | WARN 0 | SKIP 0 | PASS 856 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/biodbKegg.Rcheck/00check.log’
for details.


Installation output

biodbKegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbKegg
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbKegg)

Tests output

biodbKegg.Rcheck/tests/testthat.Rout.fail


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png'
downloaded 44 KB

[ FAIL 137 | WARN 0 | SKIP 0 | PASS 856 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (???): 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 `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(C00133 = "C00133") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure (???): 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 `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure (???): We can search for an entry by searchable field ───────────────
c(C00133 = "C00133") %in% character(0) is not TRUE

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

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0932 with mass field molecular.mass.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0932 with mass field molecular.mass.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0932 with mass field molecular.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0932 with mass field molecular.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.1032 with mass field molecular.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.1032 with mass field molecular.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0477 with mass field monoisotopic.mass.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0477 with mass field monoisotopic.mass.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0477 with mass field monoisotopic.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0477 with mass field monoisotopic.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0478 with mass field monoisotopic.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure (???): We can search for a compound ─────────────────────────────────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry C00133 by mass 89.0478 with mass field monoisotopic.mass and by name
                    D-Alanine.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(db = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure (???): annotateMzValues() accepts a single vector. ──────────────────
c("mz", id.col) not identical to colnames(ret).
Lengths differ: 2 is not 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure (???): annotateMzValues() accepts a single vector. ──────────────────
c("mz", id.col) not identical to colnames(ret).
Lengths differ: 2 is not 1
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure (???): 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 `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure (???): 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 `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure (???): Input data frame is not modified by annotateMzValues() ───────
id.col %in% colnames(ret) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id.col %in% colnames(ret))
── Failure (???): Input data frame is not modified by annotateMzValues() ───────
id.col %in% colnames(ret) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id.col %in% colnames(ret))
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggCmpnC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (test_100_compound.R:5:2): wsList() works correctly. ────────────────
length(results) > 100 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(results) > 100) at test_100_compound.R:5:8
── Failure (test_100_compound.R:12:2): wsFind() works correctly. ───────────────
!is.na(results) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(!is.na(results)) at test_100_compound.R:12:8
── Failure (test_100_compound.R:16:2): wsFind() works correctly. ───────────────
nrow(df) > 1 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(nrow(df) > 1) at test_100_compound.R:16:8
── Failure (test_100_compound.R:17:2): wsFind() works correctly. ───────────────
df[1, 1] == "cpd:C00005" is not TRUE

`actual`:   <NA>
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(df[1, 1] == "cpd:C00005") at test_100_compound.R:17:8
── Failure (test_100_compound.R:24:2): wsFind() works correctly. ───────────────
`ids` inherits from `'logical'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_is(ids, "character") at test_100_compound.R:24:8
── Failure (test_100_compound.R:26:2): wsFind() works correctly. ───────────────
ids[[1]] == "cpd:C00005" is not TRUE

`actual`:   <NA>
`expected`: TRUE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(ids[[1]] == "cpd:C00005") at test_100_compound.R:26:8
── Failure (test_100_compound.R:34:2): wsFindExactMass() works correctly. ──────
!is.na(results) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(!is.na(results)) at test_100_compound.R:34:8
── Failure (test_100_compound.R:38:2): wsFindExactMass() works correctly. ──────
nrow(df) > 1 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(nrow(df) > 1) at test_100_compound.R:38:8
── Failure (test_100_compound.R:47:2): wsFindExactMass() works correctly. ──────
all(!is.na(ids)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(all(!is.na(ids))) at test_100_compound.R:47:8
── Failure (test_100_compound.R:48:2): wsFindExactMass() works correctly. ──────
is.character(ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(is.character(ids)) at test_100_compound.R:48:8
── Failure (test_100_compound.R:54:2): wsFindExactMass() works correctly. ──────
all(!is.na(ids)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(all(!is.na(ids))) at test_100_compound.R:54:8
── Failure (test_100_compound.R:55:2): wsFindExactMass() works correctly. ──────
is.character(ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(is.character(ids)) at test_100_compound.R:55:8
── Failure (test_100_compound.R:56:2): wsFindExactMass() works correctly. ──────
length(ids) > 1 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids) > 1) at test_100_compound.R:56:8
── Failure (test_100_compound.R:64:2): wsFindMolecularWeight() works correctly. ──
!is.na(results) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(!is.na(results)) at test_100_compound.R:64:8
── Failure (test_100_compound.R:68:2): wsFindMolecularWeight() works correctly. ──
nrow(df) > 1 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(nrow(df) > 1) at test_100_compound.R:68:8
── Failure (test_100_compound.R:77:2): wsFindMolecularWeight() works correctly. ──
all(!is.na(ids)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(all(!is.na(ids))) at test_100_compound.R:77:8
── Failure (test_100_compound.R:78:2): wsFindMolecularWeight() works correctly. ──
is.character(ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(is.character(ids)) at test_100_compound.R:78:8
── Failure (test_100_compound.R:84:2): wsFindMolecularWeight() works correctly. ──
all(!is.na(ids)) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(all(!is.na(ids))) at test_100_compound.R:84:8
── Failure (test_100_compound.R:85:2): wsFindMolecularWeight() works correctly. ──
is.character(ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(is.character(ids)) at test_100_compound.R:85:8
── Failure (test_100_compound.R:86:2): wsFindMolecularWeight() works correctly. ──
length(ids) > 1 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(db = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids) > 1) at test_100_compound.R:86:8
── Failure (test_100_compound.R:137:2): getPathwayIdsPerCompound() works correctly. ──
c %in% names(ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(c %in% names(ids)) at test_100_compound.R:137:8
── Failure (test_100_compound.R:138:2): getPathwayIdsPerCompound() works correctly. ──
ids[[c]] inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_is(ids[[c]], "character") at test_100_compound.R:138:8
── Failure (test_100_compound.R:139:2): getPathwayIdsPerCompound() works correctly. ──
length(ids[[c]]) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids[[c]]) > 0) at test_100_compound.R:139:8
── Failure (test_100_compound.R:129:2): getPathwayIds() works correctly. ───────
`ids` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_is(ids, "character") at test_100_compound.R:129:8
── Failure (test_100_compound.R:130:2): getPathwayIds() works correctly. ───────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids) > 0) at test_100_compound.R:130:8
── Failure (test_100_compound.R:102:2): getPathwayIds() issue_333 is corrected ──
`ids` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_is(ids, "character") at test_100_compound.R:102:8
── Failure (test_100_compound.R:103:2): getPathwayIds() issue_333 is corrected ──
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids) > 0) at test_100_compound.R:103:8
── Failure (test_100_compound.R:104:2): getPathwayIds() issue_333 is corrected ──
any(goodpws %in% ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(any(goodpws %in% ids)) at test_100_compound.R:104:8
── Failure (test_100_compound.R:120:3): getPathwayIds() issue_338 is corrected ──
`ids` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_is(ids, "character") at test_100_compound.R:120:16
── Failure (test_100_compound.R:121:3): getPathwayIds() issue_338 is corrected ──
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids) > 0) at test_100_compound.R:121:16
── Failure (test_100_compound.R:122:3): getPathwayIds() issue_338 is corrected ──
pw %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(pw %in% ids) at test_100_compound.R:122:16
── Failure (test_100_compound.R:120:3): getPathwayIds() issue_338 is corrected ──
`ids` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_is(ids, "character") at test_100_compound.R:120:16
── Failure (test_100_compound.R:121:3): getPathwayIds() issue_338 is corrected ──
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(length(ids) > 0) at test_100_compound.R:121:16
── Failure (test_100_compound.R:122:3): getPathwayIds() issue_338 is corrected ──
pw %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─testthat::expect_true(pw %in% ids) at test_100_compound.R:122:16
── Error (test_100_compound.R:147:5): addInfo() works correctly. ───────────────
Error in `FUN(X[[i]], ...)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggCmpnC>`)
 3.   └─conn$addInfo(x, id.col = "ids", org = "mmu") at test_100_compound.R:147:4
 4.     └─self$getBiodb()$entriesFieldToVctOrLst(...)
 5.       └─base::lapply(...)
 6.         └─biodb FUN(X[[i]], ...)
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (test_200_enzyme.R:6:5): getPathwayIds() works correctly. ───────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggEnzyC>`)
 3.   └─testthat::expect_true(length(ids) > 0) at test_200_enzyme.R:6:4
── Failure (test_200_enzyme.R:34:5): issue 340 is corrected. ───────────────────
all(right_pws %in% pws) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggEnzyC>`)
 3.   └─testthat::expect_true(all(right_pws %in% pws)) at test_200_enzyme.R:34:4
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (test_300_genes.R:5:2): getPathwayIdsPerGene() works correctly. ─────
id %in% names(ids) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggGnsCn>`)
 3.   └─testthat::expect_true(id %in% names(ids)) at test_300_genes.R:5:8
── Failure (test_300_genes.R:6:2): getPathwayIdsPerGene() works correctly. ─────
ids[[id]] inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggGnsCn>`)
 3.   └─testthat::expect_is(ids[[id]], "character") at test_300_genes.R:6:8
── Failure (test_300_genes.R:7:2): getPathwayIdsPerGene() works correctly. ─────
length(ids[[id]]) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggGnsCn>`)
 3.   └─testthat::expect_true(length(ids[[id]]) > 0) at test_300_genes.R:7:8
── Failure (test_300_genes.R:13:5): getPathwayIds() works correctly. ───────────
`ids` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggGnsCn>`)
 3.   └─testthat::expect_is(ids, "character") at test_300_genes.R:13:4
── Failure (test_300_genes.R:14:5): getPathwayIds() works correctly. ───────────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggGnsCn>`)
 3.   └─testthat::expect_true(length(ids) > 0) at test_300_genes.R:14:4
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggMdlCn>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (test_600_pathway.R:7:5): getReactions() works correctly. ───────────
length(reactions) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggPthwC>`)
 3.   └─testthat::expect_true(length(reactions) > 0) at test_600_pathway.R:7:4
── Failure (test_600_pathway.R:16:5): buildPathwayGraph() works correctly. ─────
`graph` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggPthwC>`)
 3.   └─testthat::expect_is(graph, "list") at test_600_pathway.R:16:4
── Failure (test_600_pathway.R:17:5): buildPathwayGraph() works correctly. ─────
names(graph) not equal to c("vertices", "edges").
target is NULL, current is character
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggPthwC>`)
 3.   └─testthat::expect_equal(names(graph), c("vertices", "edges")) at test_600_pathway.R:17:4
── Failure (test_600_pathway.R:22:5): getPathwayIgraph() works correctly. ──────
`graph` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbKegg `<fn>`(conn = `<KggPthwC>`)
 3.   └─testthat::expect_is(graph, "igraph") at test_600_pathway.R:22:4
── Error (???): RT unit is defined when there is an RT value. ──────────────────
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(...)
 4.     └─testthat::quasi_label(enquo(object), label, arg = "object")
 5.       └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure (???): We can search for an entry by searchable field ───────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by searchable field ─────────────────
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
── Failure (???): We can search for an entry by name. ──────────────────────────
!is.null(entry) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!is.null(entry))
── Error (???): We can search for an entry by name. ────────────────────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
── Failure (???): We can load an entry from the database. ──────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─opt$refEntries$getRealEntry(id)
 4.     └─self$getRealEntries(ids = id)
 5.       └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure (???): We can load an entry from the database. ──────────────────────
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_is(e, "BiodbEntry")
── Failure (???): One wrong entry does not block the retrieval of good ones ────
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)
── Failure (???): The peak table is correct. ───────────────────────────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE

`actual`:   TRUE 
`expected`: FALSE
One of the entries is NULL.
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb `<fn>`(conn = `<KggRctnC>`, opt = `<named list>`)
 3.   └─testthat::expect_false(...)

[ FAIL 137 | WARN 0 | SKIP 0 | PASS 856 ]
Error: Test failures
Execution halted

Example timings

biodbKegg.Rcheck/biodbKegg-Ex.timings

nameusersystemelapsed
KeggCircle0.0230.0020.025
KeggCompoundConn 6.545 0.69111.523
KeggCompoundEntry1.0000.0181.023
KeggConn1.0270.0222.894
KeggEntry1.0280.0161.051
KeggEnzymeConn 8.980 0.29010.885
KeggEnzymeEntry0.9830.0151.000
KeggGenesConn1.1790.0191.203
KeggGenesEntry1.2090.0221.237
KeggGlycanConn0.6850.0140.704
KeggGlycanEntry1.1340.0231.164
KeggModuleConn1.0660.0141.084
KeggModuleEntry0.8970.0170.920
KeggOrthologyConn1.1530.0171.177
KeggOrthologyEntry1.1190.0191.148
KeggPathwayConn4.7670.0724.868
KeggPathwayEntry0.9880.0161.010
KeggReactionConn0.9200.0140.939
KeggReactionEntry0.9300.0140.948
KeggRect0.0040.0000.004
KeggShape0.0000.0000.001