R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
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Platform: x86_64-apple-darwin20

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> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbUniprot)
Warning message:
In fun(libname, pkgname) :
  Package 'biodbUniprot' is deprecated and will be removed from
  Bioconductor version 3.23
> Sys.setenv(TESTTHAT_REPORTER="summary")
> test_check("biodbUniprot")
[ FAIL 15 | WARN 0 | SKIP 0 | PASS 429 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_long_100_generic.R:16:1'): RT unit is defined when there is an RT value. ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
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$doGetEntryContentOneByOne(id)
  9.               └─base::lapply(requests, fct)
 10.                 └─biodb (local) FUN(X[[i]], ...)
 11.                   └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 12.                     └─sched::Request$new(...)
 13.                       └─sched (local) initialize(...)
 14.                         └─chk::chk_true(...)
 15.                           └─chk::abort_chk(x_name, " must be TRUE", x = x)
 16.                             └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 17.                               └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): We can search for an entry by searchable field ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
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.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): We can search for an entry by name. ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
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.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): We can load an entry from the database. ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
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$getEntryContent(ids)
  8.             └─self$getEntryContentFromDb(ch.missing.ids)
  9.               └─private$doGetEntryContentFromDb(entry.id)
 10.                 └─private$doGetEntryContentOneByOne(id)
 11.                   └─base::lapply(requests, fct)
 12.                     └─biodb (local) FUN(X[[i]], ...)
 13.                       └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 14.                         └─sched::Request$new(...)
 15.                           └─sched (local) initialize(...)
 16.                             └─chk::chk_true(...)
 17.                               └─chk::abort_chk(x_name, " must be TRUE", x = x)
 18.                                 └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 19.                                   └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): We can get a URL pointing to the entry page. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids)
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, f, FUN.VALUE = "")
 6.         └─biodbUniprot (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:16:1'): The entry page URL can be downloaded. ──
Error in `FUN(X[[i]], ...)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
 3.   └─conn$getEntryPageUrl(ref.ids[[1]])
 4.     └─private$doGetEntryPageUrl(entry.id)
 5.       └─base::vapply(id, f, FUN.VALUE = "")
 6.         └─biodbUniprot (local) FUN(X[[i]], ...)
── Error ('test_long_100_generic.R:16:1'): We can search for a compound ────────
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(db = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─db$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$getEntryContent(ids)
  7.           └─self$getEntryContentFromDb(ch.missing.ids)
  8.             └─private$doGetEntryContentFromDb(entry.id)
  9.               └─private$doGetEntryContentOneByOne(id)
 10.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$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.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$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.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$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.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): annotateMzValues() works correctly with real values. ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$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.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_100_generic.R:16:1'): Additional fields are accepted in annotateMzValues() ──
<chk_error/rlang_error/error/condition>
Error in `initialize(...)`: `chk::vld_null(encoding) || chk::vld_whole_number(encoding) || ` must be TRUE`    chk::vld_string(encoding)` must be TRUE.
Backtrace:
     ▆
  1. ├─base::do.call(fct, params)
  2. └─biodb (local) `<fn>`(conn = `<UnprtCnn>`, opt = `<named list>`)
  3.   └─conn$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.                 └─base::lapply(requests, fct)
 11.                   └─biodb (local) FUN(X[[i]], ...)
 12.                     └─self$makeRequest(method = "get", url = sched::URL$new(x), encoding = encoding)
 13.                       └─sched::Request$new(...)
 14.                         └─sched (local) initialize(...)
 15.                           └─chk::chk_true(...)
 16.                             └─chk::abort_chk(x_name, " must be TRUE", x = x)
 17.                               └─chk::err(..., n = n, tidy = tidy, class = "chk_error", call = call)
 18.                                 └─rlang::abort(msg, class = class, !!!args[named], call = call)
── Error ('test_long_200_conversions.R:98:1'): We can convert gene symbols to UniProt IDs. ──
Error in `self$wsSearch(query, retfmt = "ids", size = limit)`: object 'BiodbUrl' not found
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)
── Error ('test_long_200_conversions.R:100:1'): We can convert gene symbols to UniProt IDs. ──
Error in `self$wsSearch(query, retfmt = "ids", size = limit)`: object 'BiodbUrl' not found
Backtrace:
    ▆
 1. ├─base::do.call(fct, params)
 2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`)
 3.   └─conn$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:28:5
 4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
── Error ('test_long_200_conversions.R:102:1'): We can convert gene symbols to UniProt IDs. ──
Error in `self$wsSearch(query, retfmt = "ids", size = limit)`: object 'BiodbUrl' not found
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)

[ FAIL 15 | WARN 0 | SKIP 0 | PASS 429 ]
Error: Test failures
Execution halted

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbUniprot_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbUniprot.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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 ‘1.15.1’
* 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 ‘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 whether startup messages can be suppressed ... 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$geneSymbolToUniprotIds(names(expected_ids)) at test_long_200_conversions.R:28:5
   4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
  ── Error ('test_long_200_conversions.R:102:1'): We can convert gene symbols to UniProt IDs. ──
  Error in `self$wsSearch(query, retfmt = "ids", size = limit)`: object 'BiodbUrl' not found
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodbUniprot (local) `<fn>`(conn = `<UnprtCnn>`)
   3.   └─conn$geneSymbolToUniprotIds(names(expected_ids), ignore.nonalphanum = TRUE) at test_long_200_conversions.R:42:5
   4.     └─self$wsSearch(query, retfmt = "ids", size = limit)
  
  [ FAIL 15 | WARN 0 | SKIP 0 | PASS 429 ]
  Error: Test failures
  Execution halted
* DONE

Status: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.22-bioc-longtests/meat/biodbUniprot.Rcheck/00check.log’
for details.

* installing *source* package ‘biodbUniprot’ ...
** this is package ‘biodbUniprot’ version ‘1.15.1’
** 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
Warning in fun(libname, pkgname) :
  Package 'biodbUniprot' is deprecated and will be removed from
  Bioconductor version 3.23
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'biodbUniprot' is deprecated and will be removed from
  Bioconductor version 3.23
** testing if installed package keeps a record of temporary installation path
* DONE (biodbUniprot)