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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:topdownr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings topdownr_1.33.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/topdownr.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-16 02:45:31 UTC
* using option ‘--no-vignettes’
* checking for file ‘topdownr/DESCRIPTION’ ... OK
* this is package ‘topdownr’ version ‘1.33.0’
* 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 ‘topdownr’ 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 ... NOTE
coerce,TopDownSet-NCBSet: no visible global function definition for
  ‘subject’
show,FragmentViews: no visible global function definition for ‘subject’
Undefined global functions or variables:
  subject
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
writeMethodXmls 4.919  0.054   5.047
* 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:
  Differences:
  Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1652208 > >
  ── Failure ('test_FragmentViews.R:64:5'): constructor ──────────────────────────
  Expected `.calculateFragments("MAACE", type = "b", modifications = "Met-loss")` to equal `fv3`.
  Differences:
  Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1277953 > >
  ── Failure ('test_FragmentViews.R:73:5'): constructor ──────────────────────────
  Expected `.calculateFragments("AACE", type = "b", modifications = NULL)` to equal `fv4`.
  Differences:
  Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1277953 > >
  
  [ FAIL 5 | WARN 0 | SKIP 1 | PASS 596 ]
  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
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/topdownr.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL topdownr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘topdownr’ ...
** this is package ‘topdownr’ version ‘1.33.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (topdownr)

R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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("topdownr")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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
Loading required package: XVector
Loading required package: Seqinfo

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_check("topdownr")
Saving _problems/test_FragmentViews-44.R
Saving _problems/test_FragmentViews-48.R
Saving _problems/test_FragmentViews-57.R
Saving _problems/test_FragmentViews-66.R
Saving _problems/test_FragmentViews-74.R
[ FAIL 5 | WARN 0 | SKIP 1 | PASS 596 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1):

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_FragmentViews.R:44:5'): constructor ──────────────────────────
Expected `.calculateFragments("MAACE", type = "b")` to equal `fv`.
Differences:
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1417936 > >
── Failure ('test_FragmentViews.R:47:5'): constructor ──────────────────────────
Expected `.calculateFragments("MAACE", type = "b")` to equal `fv`.
Differences:
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1417936 > >
── Failure ('test_FragmentViews.R:55:5'): constructor ──────────────────────────
Expected `.calculateFragments("AACE", type = "b", modifications = "Acetyl")` to equal `fv2`.
Differences:
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1652208 > >
── Failure ('test_FragmentViews.R:64:5'): constructor ──────────────────────────
Expected `.calculateFragments("MAACE", type = "b", modifications = "Met-loss")` to equal `fv3`.
Differences:
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1277953 > >
── Failure ('test_FragmentViews.R:73:5'): constructor ──────────────────────────
Expected `.calculateFragments("AACE", type = "b", modifications = NULL)` to equal `fv4`.
Differences:
Attributes: < Component "elementMetadata": Attributes: < Component "listData": Component "mass": Mean relative difference: 0.1277953 > >

[ FAIL 5 | WARN 0 | SKIP 1 | PASS 596 ]
Error:
! Test failures.
Execution halted