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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:biodbHmdb.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings biodbHmdb_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbHmdb/DESCRIPTION’ ... OK
* this is package ‘biodbHmdb’ version ‘1.13.0’
* 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 ‘biodbHmdb’ can be installed ... WARNING
Found the following significant warnings:
  EntryMaker.hpp:23:21: warning: ‘EntryMaker::accession_tag’ will be initialized after [-Wreorder]
  EntryMaker.hpp:22:14: warning:   ‘bool EntryMaker::closed’ [-Wreorder]
  EntryMaker.cpp:5:1: warning:   when initialized here [-Wreorder]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 ... NOTE
Namespace in Imports field not imported from: ‘zip’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘HmdbMetabolitesConn’ ‘HmdbMetabolitesEntry’ ‘hmdbToSqlite’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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:
   3.   └─testthat::expect_equal(ids, c("HMDB0000001", "HMDB0000002")) at test_300_search.R:8:5
  ── Error ('test_300_search.R:42:1'): We can search for multiple words inside description field. ──
  Error in `entry$hasField(f)`: attempt to apply non-function
  Backtrace:
      ▆
   1. ├─base::do.call(fct, params)
   2. └─biodbHmdb (local) `<fn>`(conn = `<HmdbMtbC>`)
   3.   └─conn$searchForEntries(fields = list(description = words), max.results = 3) at test_300_search.R:11:5
   4.     └─private$doSearchForEntries(fields = fields, max.results = max.results)
   5.       └─base::vapply(names(fields), tryMatch, FUN.VALUE = TRUE)
   6.         └─biodbHmdb (local) FUN(X[[i]], ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 250 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘biodbHmdb.Rmd’ using rmarkdown

Quitting from biodbHmdb.Rmd:102-105 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Destination folder "/home/biocbuild/.cache/R/biodb/tmp" does not exist.
---
Backtrace:
    ▆
 1. └─conn$searchForEntries(list(name = "1-Methylhistidine"), max.results = 1)
 2.   └─private$doSearchForEntries(fields = fields, max.results = max.results)
 3.     └─self$getEntry(id)
 4.       └─private$bdb$getFactory()$getEntry(self$getId(), id = id, drop = drop)
 5.         └─private$loadEntries(conn$getId(), missing.ids, drop = FALSE)
 6.           └─conn$getEntryContent(ids)
 7.             └─self$download()
 8.               └─private$doExtractDownload()
 9.                 └─biodbHmdb:::extractXmlEntries(normalizePath(xml.file), normalizePath(extract.dir))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'biodbHmdb.Rmd' failed with diagnostics:
Destination folder "/home/biocbuild/.cache/R/biodb/tmp" does not exist.
--- failed re-building ‘biodbHmdb.Rmd’

SUMMARY: processing the following file failed:
  ‘biodbHmdb.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/biodbHmdb.Rcheck/00check.log’
for details.