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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MsBackendMsp.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings MsBackendMsp_1.9.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/MsBackendMsp.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'MsBackendMsp/DESCRIPTION' ... OK
* this is package 'MsBackendMsp' version '1.9.0'
* 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 'MsBackendMsp' 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 ... 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'
 OK
* 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: OK

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

R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
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(MsBackendMsp)
Loading required package: 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, table, tapply,
    union, unique, unsplit, which.max, which.min


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: BiocParallel
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> 
> ## Run specific (backend) package tests
> test_check("MsBackendMsp")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 89 ]
> 
> ## Run additional tests from Spectra:
> test_suite <- system.file("test_backends", "test_MsBackend",
+                           package = "Spectra")
> 
> fls <- system.file("extdata", "minimona.msp", package = "MsBackendMsp")
> be <- MsBackendMsp()
> be <- backendInitialize(
+     be, fls, mapping = spectraVariableMapping(MsBackendMsp(), "mona"))
> 
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W  S  OK | Context

⠏ |          0 | peaks_variables                                                
✔ |          4 | peaks_variables

⠏ |          0 | spectra_subsetting                                             
⠼ |          5 | spectra_subsetting                                             
⠴ |         16 | spectra_subsetting                                             
⠋ |         31 | spectra_subsetting                                             
⠸ |         44 | spectra_subsetting                                             
⠋ |         61 | spectra_subsetting                                             
⠴ |         76 | spectra_subsetting                                             
⠋ |         91 | spectra_subsetting                                             
⠴ |         96 | spectra_subsetting                                             
⠧ |         98 | spectra_subsetting                                             
⠏ |        100 | spectra_subsetting                                             
⠹ |        103 | spectra_subsetting                                             
⠼ |        105 | spectra_subsetting                                             
⠦ |        107 | spectra_subsetting                                             
⠇ |        109 | spectra_subsetting                                             
⠋ |        111 | spectra_subsetting                                             
⠹ |        113 | spectra_subsetting                                             
⠴ |        116 | spectra_subsetting                                             
⠇ |        119 | spectra_subsetting                                             
⠙ |        122 | spectra_subsetting                                             
⠦ |        127 | spectra_subsetting                                             
⠸ |        134 | spectra_subsetting                                             
⠋ |        141 | spectra_subsetting                                             
✔ |        141 | spectra_subsetting [2.7s]

⠏ |          0 | spectra_variables                                              
⠏ |         10 | spectra_variables                                              
⠧ |         18 | spectra_variables                                              
⠇ |         29 | spectra_variables                                              
⠦ |         37 | spectra_variables                                              
⠙ |         52 | spectra_variables                                              
⠹ |         63 | spectra_variables                                              
⠙ |         72 | spectra_variables                                              
✔ |         78 | spectra_variables [1.4s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 4.1 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 223 ]
> 
> 
> 
> 
> proc.time()
   user  system elapsed 
  11.32    5.59   16.95