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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MetaboAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MetaboAnnotation_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MetaboAnnotation.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MetaboAnnotation/DESCRIPTION’ ... OK
* this is package ‘MetaboAnnotation’ version ‘1.14.0’
* 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 ‘MetaboAnnotation’ 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MetaboAnnotation-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CompDbSource
> ### Title: Compound Annotation Sources for 'CompDb' databases
> ### Aliases: CompDbSource CompDbSource-class metadata,CompDbSource-method
> ###   show,CompDbSource-method MassBankSource
> 
> ### ** Examples
> 
> 
> ## Locate a CompDb SQLite database file. For this example we use the test
> ## database from the `CompoundDb` package.
> fl <- system.file("sql", "CompDb.MassBank.sql", package = "CompoundDb")
> ann_src <- CompDbSource(fl)
> 
> ## The object contains only the reference/link to the annotation resource.
> ann_src
Object of class CompDbSource 
Metadata information:
  - source: MassBank
  - url: https://massbank.eu/MassBank/
  - source_version: 2020.09
  - source_date: 1603272565
  - organism: NA
  - db_creation_date: Thu Oct 22 08:45:31 2020
  - supporting_package: CompoundDb
  - supporting_object: CompDb
> 
> ## Retrieve a CompDb with MassBank data for a certain MassBank release
> mb_src <- MassBankSource("2021.03")
Error in value[[3L]](cond) : failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Calls: MassBankSource ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
* 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:
      ▆
   1. └─MetaboAnnotation::MassBankSource("2021.03") at test_CompDbSource.R:53:9
   2.   └─AnnotationHub::AnnotationHub(...)
   3.     └─AnnotationHub::.Hub(...)
   4.       └─base::tryCatch(...)
   5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.             └─value[[3L]](cond)
  
  [ FAIL 3 | WARN 2 | SKIP 0 | PASS 1236 ]
  Error:
  ! Test failures.
  Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/MetaboAnnotation.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MetaboAnnotation
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MetaboAnnotation’ ...
** this is package ‘MetaboAnnotation’ version ‘1.14.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (MetaboAnnotation)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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(MetaboAnnotation)
> library(msdata)
> library(Spectra)
Loading required package: S4Vectors
Loading required package: stats4
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


Attaching package: 'S4Vectors'

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

    endoapply

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

    findMatches

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

    I, expand.grid, unname

Loading required package: BiocParallel
> library(testthat)
> 
> fl <- system.file("TripleTOF-SWATH", "PestMix1_DDA.mzML", package = "msdata")
> pest_ms2 <- filterMsLevel(Spectra(fl), 2L)
> pest_ms2 <- pest_ms2[c(808, 809, 945:955)]
> load(system.file("extdata", "minimb.RData", package = "MetaboAnnotation"))
> 
> test_check("MetaboAnnotation")
Saving _problems/test_CompDbSource-50.R
Saving _problems/test_CompDbSource-51.R
Saving _problems/test_CompDbSource-53.R
[ FAIL 3 | WARN 2 | SKIP 0 | PASS 1236 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_CompDbSource.R:50:9'): MassBankSource works with AnnotationHub ──
`MassBankSource(release = "other")` threw an error with unexpected message.
Expected match: "not found"
Actual message: "failed to connect\n  reason: Failed to perform HTTP request.\nCaused by error in `curl::curl_fetch_memory()`:\n! Timeout was reached [bioconductor.org]:\nSSL connection timeout\n  Consider rerunning with 'localHub=TRUE'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(MassBankSource(release = "other"), "not found") at test_CompDbSource.R:50:9
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MetaboAnnotation::MassBankSource(release = "other")
  7.   └─AnnotationHub::AnnotationHub(...)
  8.     └─AnnotationHub::.Hub(...)
  9.       └─base::tryCatch(...)
 10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             └─value[[3L]](cond)
── Failure ('test_CompDbSource.R:51:9'): MassBankSource works with AnnotationHub ──
`MassBankSource(release = "")` threw an error with unexpected message.
Expected match: "ambiguous"
Actual message: "failed to connect\n  reason: Failed to perform HTTP request.\nCaused by error in `curl::curl_fetch_memory()`:\n! Timeout was reached [bioconductor.org]:\nSSL connection timeout\n  Consider rerunning with 'localHub=TRUE'"
Backtrace:
     ▆
  1. ├─testthat::expect_error(MassBankSource(release = ""), "ambiguous") at test_CompDbSource.R:51:9
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. └─MetaboAnnotation::MassBankSource(release = "")
  7.   └─AnnotationHub::AnnotationHub(...)
  8.     └─AnnotationHub::.Hub(...)
  9.       └─base::tryCatch(...)
 10.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 11.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 12.             └─value[[3L]](cond)
── Error ('test_CompDbSource.R:53:9'): MassBankSource works with AnnotationHub ──
Error in `value[[3L]](cond)`: failed to connect
  reason: Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [bioconductor.org]:
SSL connection timeout
  Consider rerunning with 'localHub=TRUE'
Backtrace:
    ▆
 1. └─MetaboAnnotation::MassBankSource("2021.03") at test_CompDbSource.R:53:9
 2.   └─AnnotationHub::AnnotationHub(...)
 3.     └─AnnotationHub::.Hub(...)
 4.       └─base::tryCatch(...)
 5.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 6.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 7.             └─value[[3L]](cond)

[ FAIL 3 | WARN 2 | SKIP 0 | PASS 1236 ]
Error:
! Test failures.
Warning message:
call dbDisconnect() when finished working with a connection 
Execution halted