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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:struct.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings struct_1.17.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/struct.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 'struct/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'struct' version '1.17.0'
* 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 'struct' 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 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 ... NOTE
checkRd: (-1) set_obj_show.Rd:12: Lost braces
    12 | \item{extra_string}{a function that returns an extra string using the input object as an input e.g. function(object){return = 'extra_string'}}
       |                                                                                                                     ^
* 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 files in 'vignettes' ... OK
* checking examples ... OK
* 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:
    6.       │ └─rols:::.Ontology(...)
    7.       │   └─methods::new(`<chr>`, ...)
    8.       │     ├─methods::initialize(value, ...)
    9.       │     └─methods::initialize(value, ...)
   10.       ├─httr2::resp_body_json(req_perform(request(url)))
   11.       │ └─httr2:::check_response(resp)
   12.       │   └─httr2:::is_response(resp)
   13.       └─httr2::req_perform(request(url))
   14.         └─httr2:::handle_resp(req, resp, error_call = error_call)
   15.           └─httr2:::resp_abort(resp, req, body, call = error_call)
   16.             └─rlang::abort(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 128 ]
  Error: Test failures
  Execution halted
* 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: 1 ERROR, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/struct.Rcheck/00check.log'
for details.

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

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)
> library(struct)
> library(SummarizedExperiment)
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> 
> test_check("struct")
[ FAIL 1 | WARN 1 | SKIP 0 | PASS 128 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-ontology.R:3:5'): ontology works as expected ───────────────────
<httr2_http_500/httr2_http/httr2_error/rlang_error/error/condition>
Error in `req_perform(request(url))`: HTTP 500 Internal Server Error.
Backtrace:
     ▆
  1. └─struct::ontology_term("STATO:0000555", rols = FALSE) at test-ontology.R:3:5
  2.   ├─rols::Ontology(ontology)
  3.   └─rols::Ontology(ontology)
  4.     └─rols:::makeOntology(url)
  5.       ├─rols:::ontologyFromJson(resp_body_json(req_perform(request(url))))
  6.       │ └─rols:::.Ontology(...)
  7.       │   └─methods::new(`<chr>`, ...)
  8.       │     ├─methods::initialize(value, ...)
  9.       │     └─methods::initialize(value, ...)
 10.       ├─httr2::resp_body_json(req_perform(request(url)))
 11.       │ └─httr2:::check_response(resp)
 12.       │   └─httr2:::is_response(resp)
 13.       └─httr2::req_perform(request(url))
 14.         └─httr2:::handle_resp(req, resp, error_call = error_call)
 15.           └─httr2:::resp_abort(resp, req, body, call = error_call)
 16.             └─rlang::abort(...)

[ FAIL 1 | WARN 1 | SKIP 0 | PASS 128 ]
Error: Test failures
Execution halted