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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MobilityTransformR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MobilityTransformR_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MobilityTransformR.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MobilityTransformR/DESCRIPTION’ ... OK
* this is package ‘MobilityTransformR’ version ‘1.7.1’
* 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 ‘MobilityTransformR’ 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 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 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:
   10. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   11. └─MobilityTransformR::getMtime(...)
   12.   ├─base::as.data.frame(...)
   13.   ├─xcms::chromPeaks(...)
   14.   └─xcms::chromPeaks(...)
   15.     └─xcms (local) .local(object, ...)
   16.       └─xcms:::.index_chrom_peaks(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ]
  Error: Test failures
  In addition: Warning message:
  In fun(libname, pkgname) :
    Package 'MobilityTransformR' is deprecated and will be removed from
    Bioconductor version 3.20
  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: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/MobilityTransformR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MobilityTransformR
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘MobilityTransformR’ ...
** using staged installation
** R
** 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
Warning in fun(libname, pkgname) :
  Package 'MobilityTransformR' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'MobilityTransformR' is deprecated and will be removed from
  Bioconductor version 3.20
** testing if installed package keeps a record of temporary installation path
* DONE (MobilityTransformR)

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 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("testthat")
> 
> test_check("MobilityTransformR")
Loading required package: MobilityTransformR
Loading required package: MSnbase
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: Biobase
Welcome to Bioconductor

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

Loading required package: mzR
Loading required package: Rcpp
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: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth


This is MSnbase version 2.29.4 
  Visit https://lgatto.github.io/MSnbase/ to get started.
 Consider switching to the 'R for Mass Spectrometry'
 packages - see https://RforMassSpectrometry.org for details.


Attaching package: 'MSnbase'

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

    trimws

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_getMt.R:46:5'): Getting migration time works ─────────────────
`getMtime(raw_data, mz = c(150.001, 150.002), mt = mt_paracetamol)` threw an error with unexpected message.
Expected match: "0 peaks have been found in file 1, align input parameters"
Actual message: "invalid 'times' argument"
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test_getMt.R:46:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─testthat::expect_error(...)
  7. │ └─testthat:::quasi_capture(...)
  8. │   ├─testthat (local) .capture(...)
  9. │   │ └─base::withCallingHandlers(...)
 10. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 11. └─MobilityTransformR::getMtime(...)
 12.   ├─base::as.data.frame(...)
 13.   ├─xcms::chromPeaks(...)
 14.   └─xcms::chromPeaks(...)
 15.     └─xcms (local) .local(object, ...)
 16.       └─xcms:::.index_chrom_peaks(...)
── Failure ('test_getMt.R:89:5'): Getting migration time with CentWaveParam works ──
`getMtime(raw_data, mz = c(150.001, 150.002), mt = mt_paracetamol)` threw an error with unexpected message.
Expected match: "0 peaks have been found in file 1, align input parameters"
Actual message: "invalid 'times' argument"
Backtrace:
     ▆
  1. ├─testthat::expect_warning(...) at test_getMt.R:89:5
  2. │ └─testthat:::quasi_capture(...)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─testthat::expect_error(...)
  7. │ └─testthat:::quasi_capture(...)
  8. │   ├─testthat (local) .capture(...)
  9. │   │ └─base::withCallingHandlers(...)
 10. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
 11. └─MobilityTransformR::getMtime(...)
 12.   ├─base::as.data.frame(...)
 13.   ├─xcms::chromPeaks(...)
 14.   └─xcms::chromPeaks(...)
 15.     └─xcms (local) .local(object, ...)
 16.       └─xcms:::.index_chrom_peaks(...)

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 66 ]
Error: Test failures
In addition: Warning message:
In fun(libname, pkgname) :
  Package 'MobilityTransformR' is deprecated and will be removed from
  Bioconductor version 3.20
Execution halted