Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-04 23:55:02 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
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 9/33HostnameOS / ArchCHECK
biodbKegg 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-04 09:55:02 -0400 (Sat, 04 May 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  ERROR  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR  

CHECK results for biodbKegg on palomino3


To the developers/maintainers of the biodbKegg package:
- 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: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbKegg_1.10.0.tar.gz
StartedAt: 2024-05-04 16:05:45 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 16:09:36 -0400 (Sat, 04 May 2024)
EllapsedTime: 230.7 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbKegg.Rcheck
Warnings: NA

Tests output

biodbKegg.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> # 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 5 | WARN 1 | SKIP 0 | PASS 1673 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_350_glycan.R:16:1'): We can search for an entry by searchable field ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<KggGlycC>`, opt = `<named list>`)
  3.   └─conn$searchForEntries(fields = x, max.results = max.results)
  4.     └─private$doSearchForEntries(fields = fields, max.results = max.results)
  5.       └─private$filterOnReferences(...)
  6.         └─self$getEntry(id)
  7.           └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  8.             └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  9.               └─conn$getEntryContent(ids)
 10.                 └─self$getEntryContentFromDb(ch.missing.ids)
 11.                   └─private$doGetEntryContentFromDb(entry.id)
 12.                     └─private$doGetEntryContentOneByOne(id)
 13.                       └─scheduler$sendRequest(requests[[i]])
 14.                         └─cch$saveContentToFile(...)
 15.                           └─private$doSaveContentToFile(...)
 16.                             └─biodb:::saveContentsToFiles(file.paths, content)
 17.                               └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 18.                                 └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 19.                                   └─base::cat(cnt, file = f)
 20.                                     └─base::file(file, ifelse(append, "a", "w"))
── Failure ('test_long_500_orthology.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 = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0)
── Failure ('test_long_500_orthology.R:16:1'): We can search for an entry by searchable field ──
c(K12668 = "K12668") %in% character(0) is not TRUE

`actual`:   FALSE
`expected`: TRUE 
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_long_500_orthology.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 K12668 by name "dolichyl-diphosphooligosaccharide---protein glycosyltransferase subunit DAD1/OST2".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_long_500_orthology.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 K12668 by name "dolichyl-diphosphooligosaccharide---protein glycosyltransferase subunit DAD1/OST2".
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
 3.   └─testthat::expect_true(id %in% ids, msg)

[ FAIL 5 | WARN 1 | SKIP 0 | PASS 1673 ]
Error: Test failures
Execution halted

'R CMD check' output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbKegg_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbKegg.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 '1.10.0'
* 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 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 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:
  ── Failure ('test_long_500_orthology.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 K12668 by name "dolichyl-diphosphooligosaccharide---protein glycosyltransferase subunit DAD1/OST2".
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodb (local) `<fn>`(conn = `<KggOrthC>`, opt = `<named list>`)
   3.   └─testthat::expect_true(id %in% ids, msg)
  
  [ FAIL 5 | WARN 1 | SKIP 0 | PASS 1673 ]
  Error: Test failures
  Execution halted
* DONE

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


Installation output

biodbKegg.Rcheck/00install.out

* 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)