Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 203/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbKegg 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/biodbKegg
git_branch: RELEASE_3_19
git_last_commit: b3eb46e
git_last_commit_date: 2024-04-30 11:38:33 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for biodbKegg on nebbiolo1

To the developers/maintainers of the biodbKegg package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biodbKegg
Version: 1.10.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbKegg_1.10.0.tar.gz
StartedAt: 2024-06-19 21:01:45 -0400 (Wed, 19 Jun 2024)
EndedAt: 2024-06-19 21:26:42 -0400 (Wed, 19 Jun 2024)
EllapsedTime: 1496.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbKegg.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:biodbKegg.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings biodbKegg_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biodbKegg.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbKegg/DESCRIPTION’ ... OK
* this is package ‘biodbKegg’ version ‘1.10.0’
* 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 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   15.079  0.505 123.583
KeggPathwayConn   6.739  0.545  55.347
KeggCompoundConn  2.456  0.069  14.359
* 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 26 | WARN 0 | SKIP 0 | PASS 1454 ]
  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-3.19-bioc/meat/biodbKegg.Rcheck/00check.log’
for details.


Installation output

biodbKegg.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL biodbKegg
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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
** 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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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)
> Sys.setenv(TESTTHAT_REPORTER = "summary")
> test_check("biodbKegg")
trying URL 'https://www.kegg.jp/kegg/pathway/map/map00260.png?17188466411047487'
downloaded 158 KB

[ FAIL 26 | WARN 0 | SKIP 0 | PASS 1454 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_200_enzyme.R:74:1'): 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 = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_200_enzyme.R:74:1'): We can search for an entry by searchable field ──
c(`1.1.1.165` = "1.1.1.165") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_200_enzyme.R:74:1'): We can search for an entry by name. ─────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry 1.1.1.165 by name "2-alkyn-1-ol dehydrogenase".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_200_enzyme.R:74:1'): We can search for an entry by name. ─────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry 1.1.1.165 by name "2-alkyn-1-ol dehydrogenase".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggEnzyC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── 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_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_300_genes.R:32:1'): We can search for an entry by name. ──────
length(ids) > 0 is not TRUE

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

`actual`:   FALSE
`expected`: TRUE 
While searching for entry mmu:14635 by name "(RefSeq) galactokinase 1".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggGnsCn>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_350_glycan.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 = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_350_glycan.R:16:1'): We can search for an entry by searchable field ──
c(G00018 = "G00018") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_350_glycan.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 G00018 by name "DS 3".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_350_glycan.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 G00018 by name "DS 3".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── 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:88:1'): 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 = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_600_pathway.R:88:1'): We can search for an entry by searchable field ──
c(map00053 = "map00053") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_600_pathway.R:88:1'): We can search for an entry by name. ────
length(ids) > 0 is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry map00053 by name "Ascorbate and aldarate metabolism".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_600_pathway.R:88:1'): We can search for an entry by name. ────
id %in% ids is not TRUE

`actual`:   FALSE
`expected`: TRUE 
While searching for entry map00053 by name "Ascorbate and aldarate metabolism".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggPthwC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)
── 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 26 | WARN 0 | SKIP 0 | PASS 1454 ]
Error: Test failures
Execution halted

Example timings

biodbKegg.Rcheck/biodbKegg-Ex.timings

nameusersystemelapsed
KeggCircle0.0040.0030.007
KeggCompoundConn 2.456 0.06914.359
KeggCompoundEntry0.3470.0241.862
KeggConn0.3170.0162.422
KeggEntry0.1620.0040.165
KeggEnzymeConn 15.079 0.505123.583
KeggEnzymeEntry0.3430.0361.866
KeggGenesConn0.4160.0001.872
KeggGenesEntry0.2040.0010.204
KeggGlycanConn0.1730.0520.224
KeggGlycanEntry0.3450.0101.845
KeggModuleConn0.3270.0071.816
KeggModuleEntry0.2350.0760.311
KeggOrthologyConn0.4300.0372.300
KeggOrthologyEntry0.2850.0040.289
KeggPathwayConn 6.739 0.54555.347
KeggPathwayEntry0.3200.0051.809
KeggReactionConn0.4010.0001.875
KeggReactionEntry0.2010.0650.265
KeggRect0.0030.0000.003
KeggShape0.0010.0000.001