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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MeSHDbi.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MeSHDbi_1.41.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/MeSHDbi.Rcheck'
* using R version 4.4.1 (2024-06-14 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 option '--no-vignettes'
* checking for file 'MeSHDbi/DESCRIPTION' ... OK
* this is package 'MeSHDbi' version '1.41.0'
* 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 'MeSHDbi' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL MeSHDbi
###
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* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'MeSHDbi' ...
** 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 (MeSHDbi)

R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
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.

> library("testthat")
> 
> # Setting
> options(testthat.use_colours = FALSE)
> 
> test_file("testthat/test_methods.R")

══ Testing test_methods.R ══════════════════════════════════════════════════════

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 2 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ]

── Failure ('test_methods.R:27:1'): (code run outside of `test_that()`) ────────
species(MeSH.Sil.eg.db) != "" is not TRUE

`actual`:   <NA>
`expected`: TRUE

── Failure ('test_methods.R:30:1'): (code run outside of `test_that()`) ────────
nomenclature(MeSH.Sil.eg.db) != "" is not TRUE

`actual`:   <NA>
`expected`: TRUE

── Error ('test_methods.R:33:1'): (code run outside of `test_that()`) ──────────
Error: no such table: DATA
Backtrace:
     ▆
  1. ├─testthat::expect_true(...) at test_methods.R:33:1
  2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─MeSHDbi::listDatabases(MeSH.Sil.eg.db)
  5. └─MeSHDbi::listDatabases(MeSH.Sil.eg.db)
  6.   ├─DBI::dbGetQuery(x$conn, "SELECT DISTINCT SOURCEDB FROM DATA;")
  7.   └─DBI::dbGetQuery(x$conn, "SELECT DISTINCT SOURCEDB FROM DATA;")
  8.     └─DBI (local) .local(conn, statement, ...)
  9.       ├─DBI::dbSendQuery(conn, statement, ...)
 10.       └─RSQLite::dbSendQuery(conn, statement, ...)
 11.         └─RSQLite (local) .local(conn, statement, ...)
 12.           ├─methods::new(...)
 13.           │ ├─methods::initialize(value, ...)
 14.           │ └─methods::initialize(value, ...)
 15.           └─RSQLite:::result_create(conn@ptr, statement)

[ FAIL 3 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
   8.32    1.46   10.57