##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings MsQuality_0.99.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MsQuality.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘0.99.8’
* 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 ‘MsQuality’ 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 R 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘MsQuality-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateMetrics
> ### Title: Calculate QC metrics from a Spectra object
> ### Aliases: calculateMetrics
> 
> ### ** Examples
> 
> library(msdata)
> library(Spectra)
Loading required package: S4Vectors
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth

> fls <- dir(system.file("sciex", package = "msdata"), full.names = TRUE)
> spectra <- Spectra(fls, backend = MsBackendMzR())
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
Calls: Spectra ... initialize -> initialize -> backendInitialize -> MsBackendMzR
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:
    6. │   │   └─base::eval(call, callEnv)
    7. │   ├─Spectra (local) .nextMethod(...)
    8. │   │ └─Spectra (local) .local(object, ...)
    9. │   │   ├─methods::new(...)
   10. │   │   │ ├─methods::initialize(value, ...)
   11. │   │   │ └─methods::initialize(value, ...)
   12. │   │   └─Spectra::backendInitialize(...)
   13. │   └─Spectra::MsBackendMzR()
   14. │     └─base::stop(...)
   15. └─base::.handleSimpleError(...)
   16.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MsQuality.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/MsQuality.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MsQuality
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘MsQuality’ ...
** using staged installation
** R
** data
** 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 (MsQuality)

R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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("MsQuality")
> library("Spectra")
Loading required package: S4Vectors
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> library("msdata")
> library("S4Vectors")
> 
> test_check("MsQuality")
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_function_Spectra_metrics.R:4:1'): (code run outside of `test_that()`) ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
Backtrace:
     ▆
  1. ├─Spectra::Spectra(fls, backend = MsBackendMzR()) at test_function_Spectra_metrics.R:4:0
  2. ├─Spectra::Spectra(fls, backend = MsBackendMzR())
  3. │ └─Spectra (local) .local(object, ...)
  4. │   ├─methods::callNextMethod(...)
  5. │   │ └─base::eval(call, callEnv)
  6. │   │   └─base::eval(call, callEnv)
  7. │   ├─Spectra (local) .nextMethod(...)
  8. │   │ └─Spectra (local) .local(object, ...)
  9. │   │   ├─methods::new(...)
 10. │   │   │ ├─methods::initialize(value, ...)
 11. │   │   │ └─methods::initialize(value, ...)
 12. │   │   └─Spectra::backendInitialize(...)
 13. │   └─Spectra::MsBackendMzR()
 14. │     └─base::stop(...)
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))
── Error ('test_function_Spectra_qualityMetrics.R:5:1'): (code run outside of `test_that()`) ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
Backtrace:
     ▆
  1. ├─Spectra::Spectra(fls, backend = MsBackendMzR()) at test_function_Spectra_qualityMetrics.R:5:0
  2. ├─Spectra::Spectra(fls, backend = MsBackendMzR())
  3. │ └─Spectra (local) .local(object, ...)
  4. │   ├─methods::callNextMethod(...)
  5. │   │ └─base::eval(call, callEnv)
  6. │   │   └─base::eval(call, callEnv)
  7. │   ├─Spectra (local) .nextMethod(...)
  8. │   │ └─Spectra (local) .local(object, ...)
  9. │   │   ├─methods::new(...)
 10. │   │   │ ├─methods::initialize(value, ...)
 11. │   │   │ └─methods::initialize(value, ...)
 12. │   │   └─Spectra::backendInitialize(...)
 13. │   └─Spectra::MsBackendMzR()
 14. │     └─base::stop(...)
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))
── Error ('test_function_calculateMetrics_from_Spectra.R:2:1'): (code run outside of `test_that()`) ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
Backtrace:
     ▆
  1. ├─Spectra::Spectra(fls, backend = MsBackendMzR()) at test_function_calculateMetrics_from_Spectra.R:2:0
  2. ├─Spectra::Spectra(fls, backend = MsBackendMzR())
  3. │ └─Spectra (local) .local(object, ...)
  4. │   ├─methods::callNextMethod(...)
  5. │   │ └─base::eval(call, callEnv)
  6. │   │   └─base::eval(call, callEnv)
  7. │   ├─Spectra (local) .nextMethod(...)
  8. │   │ └─Spectra (local) .local(object, ...)
  9. │   │   ├─methods::new(...)
 10. │   │   │ ├─methods::initialize(value, ...)
 11. │   │   │ └─methods::initialize(value, ...)
 12. │   │   └─Spectra::backendInitialize(...)
 13. │   └─Spectra::MsBackendMzR()
 14. │     └─base::stop(...)
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))
── Error ('test_function_visualizations.R:5:1'): (code run outside of `test_that()`) ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'object' in selecting a method for function 'backendInitialize': The use of 'MsBackendMzR' requires package 'mzR'. Please install with 'BiocInstaller::install("mzR")'
Backtrace:
     ▆
  1. ├─Spectra::Spectra(fls, backend = MsBackendMzR()) at test_function_visualizations.R:5:0
  2. ├─Spectra::Spectra(fls, backend = MsBackendMzR())
  3. │ └─Spectra (local) .local(object, ...)
  4. │   ├─methods::callNextMethod(...)
  5. │   │ └─base::eval(call, callEnv)
  6. │   │   └─base::eval(call, callEnv)
  7. │   ├─Spectra (local) .nextMethod(...)
  8. │   │ └─Spectra (local) .local(object, ...)
  9. │   │   ├─methods::new(...)
 10. │   │   │ ├─methods::initialize(value, ...)
 11. │   │   │ └─methods::initialize(value, ...)
 12. │   │   └─Spectra::backendInitialize(...)
 13. │   └─Spectra::MsBackendMzR()
 14. │     └─base::stop(...)
 15. └─base::.handleSimpleError(...)
 16.   └─base (local) h(simpleError(msg, call))

[ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted