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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings MsBackendRawFileReader_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.4.0’
* 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 ‘MsBackendRawFileReader’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
ioBenchmark 36.987  4.875  14.911
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘MsBackendRawFileReader.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘MsBackendRawFileReader’ ...
** using staged installation
** R
** 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 (MsBackendRawFileReader)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
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("MsBackendRawFileReader")
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, 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("Spectra")
> 
> 
> sample_raw_file <- file.path(system.file(package = "rawrr"),
+                                 'extdata', 'sample.raw')
> 
> sample_mzXML_file <- file.path(path.package(package = 'MsBackendRawFileReader'),
+                                 'extdata', 'sample.mzXML')
> 
> 
> sample_raw <-  backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(), files = sample_raw_file)
> 
> 
> #sample_mzr <-  backendInitialize(MsBackendMzR(), files = sample_mzXML_file)
> 
> 
> mgf_file <- file.path(system.file(package = "MsBackendRawFileReader"),
+                              'extdata', '3159619b11ed_4590_9594.mgf')
> 
> 
> rv <- lapply(1:2, function(x){
+   file.copy(from = sample_raw_file, to = tempfile(fileext='.raw'))})
> 
> 
> register(SnowParam(workers = 1, type = "SOCK") , default = TRUE); 
> sample_raw_2 <- backendInitialize(MsBackendRawFileReader(),
+     files = file.path(tempdir(),
+          list.files(path = tempdir(), pattern = 'raw$')))
> 
> 
> test_check("MsBackendRawFileReader")
[ FAIL 0 | WARN 1 | SKIP 2 | PASS 9 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• isFALSE(file.exists(sample_mzXML_file)) is TRUE (1)
• isFALSE(require(MsBackendRawMgf)) is TRUE (1)

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 9 ]
> 
> 
> be <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
+                                  files = c(sample_raw_file))
> 
> ## Run the MsBackend spectra variable test suite
> test_suite <- system.file("test_backends", "test_MsBackend",
+                           package = "Spectra")
> 
> #res <- test_file(paste0(test_suite, "/test_spectra_variables.R"),
> #                 reporter = check_reporter(), stop_on_failure = TRUE)
> 
> 
> ## Run the whole suite.
> res <- test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S  OK | Context

⠏ |         0 | spectra_variables                                               
⠙ |        12 | spectra_variables                                               
⠸ |        14 | spectra_variables                                               
⠴ |        16 | spectra_variables                                               
⠙ |        42 | spectra_variables                                               
⠹ |        43 | spectra_variables                                               
✔ |     1  59 | spectra_variables [8.9s]
────────────────────────────────────────────────────────────────────────────────
Skip ('test_spectra_variables.R:262:1'): spectraNames
Reason: empty test
────────────────────────────────────────────────────────────────────────────────

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 9.0 s

── Skipped tests  ──────────────────────────────────────────────────────────────
• empty test (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 59 ]

🔥 Your tests are lit 🔥
> 
> proc.time()
   user  system elapsed 
 30.223   3.489  31.179