Back to Long Tests report for BioC 3.19

This page was generated on 2024-05-11 23:55:02 -0400 (Sat, 11 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4751
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4485
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4515
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 13/33HostnameOS / ArchCHECK
biodbUniprot 1.10.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-05-11 09:55:01 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/biodbUniprot
git_branch: RELEASE_3_19
git_last_commit: e07b420
git_last_commit_date: 2024-04-30 11:38:08 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK  
palomino3Windows Server 2022 Datacenter / x64  ERROR  
lconwaymacOS 12.7.1 Monterey / x86_64  OK  

CHECK results for biodbUniprot on palomino3


To the developers/maintainers of the biodbUniprot 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: biodbUniprot
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 biodbUniprot_1.10.0.tar.gz
StartedAt: 2024-05-11 16:10:24 -0400 (Sat, 11 May 2024)
EndedAt: 2024-05-11 16:11:48 -0400 (Sat, 11 May 2024)
EllapsedTime: 83.8 seconds
RetCode: 1
Status:   ERROR  
CheckDir: biodbUniprot.Rcheck
Warnings: NA

Tests output

biodbUniprot.Rcheck/tests/testthat.Rout.fail


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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Type 'license()' or 'licence()' for distribution details.

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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
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Type 'q()' to quit R.

> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbUniprot)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodbUniprot")
[ FAIL 13 | WARN 12 | SKIP 0 | PASS 497 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:16:1'): RT unit is defined when there is an RT value. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getBiodb()$getFactory()$getEntry(...)
  4.     └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  5.       └─conn$getEntryContent(ids)
  6.         └─self$getEntryContentFromDb(ch.missing.ids)
  7.           └─private$doGetEntryContentFromDb(entry.id)
  8.             └─private$doGetEntryContentOneByOne(id)
  9.               └─scheduler$sendRequest(requests[[i]])
 10.                 └─cch$saveContentToFile(...)
 11.                   └─private$doSaveContentToFile(...)
 12.                     └─biodb:::saveContentsToFiles(file.paths, content)
 13.                       └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 14.                         └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 15.                           └─base::cat(cnt, file = f)
 16.                             └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.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 = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─cch$saveContentToFile(...)
  8.             └─private$doSaveContentToFile(...)
  9.               └─biodb:::saveContentsToFiles(file.paths, content)
 10.                 └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 11.                   └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 12.                     └─base::cat(cnt, file = f)
 13.                       └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): We can search for an entry by name. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─cch$saveContentToFile(...)
  8.             └─private$doSaveContentToFile(...)
  9.               └─biodb:::saveContentsToFiles(file.paths, content)
 10.                 └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 11.                   └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 12.                     └─base::cat(cnt, file = f)
 13.                       └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): We can load an entry from the database. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─opt$refEntries$getRealEntry(id)
  4.     └─self$getRealEntries(ids = id)
  5.       └─private$bdb$getFactory()$getEntry(...)
  6.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  7.           └─conn$getEntryContent(ids)
  8.             └─cch$saveContentToFile(...)
  9.               └─private$doSaveContentToFile(...)
 10.                 └─biodb:::saveContentsToFiles(file.paths, content)
 11.                   └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 12.                     └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 13.                       └─base::cat(cnt, file = f)
 14.                         └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): We can search for a compound ────────
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─db$getEntry(id, drop = TRUE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─cch$saveContentToFile(...)
  8.             └─private$doSaveContentToFile(...)
  9.               └─biodb:::saveContentsToFiles(file.paths, content)
 10.                 └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 11.                   └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 12.                     └─base::cat(cnt, file = f)
 13.                       └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─scheduler$sendRequest(requests[[i]])
 11.                   └─cch$saveContentToFile(...)
 12.                     └─private$doSaveContentToFile(...)
 13.                       └─biodb:::saveContentsToFiles(file.paths, content)
 14.                         └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 15.                           └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 16.                             └─base::cat(cnt, file = f)
 17.                               └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─scheduler$sendRequest(requests[[i]])
 11.                   └─cch$saveContentToFile(...)
 12.                     └─private$doSaveContentToFile(...)
 13.                       └─biodb:::saveContentsToFiles(file.paths, content)
 14.                         └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 15.                           └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 16.                             └─base::cat(cnt, file = f)
 17.                               └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─scheduler$sendRequest(requests[[i]])
 11.                   └─cch$saveContentToFile(...)
 12.                     └─private$doSaveContentToFile(...)
 13.                       └─biodb:::saveContentsToFiles(file.paths, content)
 14.                         └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 15.                           └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 16.                             └─base::cat(cnt, file = f)
 17.                               └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): annotateMzValues() works correctly with real values. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$getEntry(ids, drop = FALSE)
  4.     └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
  5.       └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
  6.         └─conn$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─scheduler$sendRequest(requests[[i]])
 11.                   └─cch$saveContentToFile(...)
 12.                     └─private$doSaveContentToFile(...)
 13.                       └─biodb:::saveContentsToFiles(file.paths, content)
 14.                         └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 15.                           └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 16.                             └─base::cat(cnt, file = f)
 17.                               └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_100_generic.R:16:1'): Additional fields are accepted in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
 3.   └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
 4.     └─biodb (local) FUN(X[[i]], ...)
── Error ('test_long_200_conversions.R:98:1'): We can convert gene symbols to UniProt IDs. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`)
  3.   └─conn$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:14:5
  4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
  5.       └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  6.         └─cch$saveContentToFile(...)
  7.           └─private$doSaveContentToFile(...)
  8.             └─biodb:::saveContentsToFiles(file.paths, content)
  9.               └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 10.                 └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 11.                   └─base::cat(cnt, file = f)
 12.                     └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_200_conversions.R:100:1'): We can convert gene symbols to UniProt IDs. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`)
  3.   └─conn$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:28:5
  4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
  5.       └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  6.         └─cch$saveContentToFile(...)
  7.           └─private$doSaveContentToFile(...)
  8.             └─biodb:::saveContentsToFiles(file.paths, content)
  9.               └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 10.                 └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 11.                   └─base::cat(cnt, file = f)
 12.                     └─base::file(file, ifelse(append, "a", "w"))
── Error ('test_long_200_conversions.R:102:1'): We can convert gene symbols to UniProt IDs. ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`)
  3.   └─conn$geneSymbolToUniprotIds(names(expected_ids), ignore.nonalphanum = TRUE) at test_long_200_conversions.R:42:5
  4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
  5.       └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
  6.         └─cch$saveContentToFile(...)
  7.           └─private$doSaveContentToFile(...)
  8.             └─biodb:::saveContentsToFiles(file.paths, content)
  9.               └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
 10.                 └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
 11.                   └─base::cat(cnt, file = f)
 12.                     └─base::file(file, ifelse(append, "a", "w"))

[ FAIL 13 | WARN 12 | SKIP 0 | PASS 497 ]
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 biodbUniprot_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc-longtests/meat/biodbUniprot.Rcheck'
* using R version 4.4.0 (2024-04-24 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 'biodbUniprot/DESCRIPTION' ... OK
* this is package 'biodbUniprot' 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 'biodbUniprot' 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:
    2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`)
    3.   └─conn$geneSymbolToUniprotIds(names(expected_ids), ignore.nonalphanum = TRUE) at test_long_200_conversions.R:42:5
    4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
    5.       └─self$getBiodb()$getRequestScheduler()$sendRequest(request)
    6.         └─cch$saveContentToFile(...)
    7.           └─private$doSaveContentToFile(...)
    8.             └─biodb:::saveContentsToFiles(file.paths, content)
    9.               └─base::mapply(function(cnt, f) cat(cnt, file = f), contents, files)
   10.                 └─biodb (local) `<fn>`(dots[[1L]][[1L]], dots[[2L]][[1L]])
   11.                   └─base::cat(cnt, file = f)
   12.                     └─base::file(file, ifelse(append, "a", "w"))
  
  [ FAIL 13 | WARN 12 | SKIP 0 | PASS 497 ]
  Error: Test failures
  Execution halted
* DONE

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

Installation output

biodbUniprot.Rcheck/00install.out

* installing *source* package 'biodbUniprot' ...
** 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 (biodbUniprot)