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This page was generated on 2025-04-22 13:18 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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Package 1361/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendRawFileReader 1.14.0  (landing page)
Christian Panse
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/MsBackendRawFileReader
git_branch: RELEASE_3_21
git_last_commit: a5e44a0
git_last_commit_date: 2025-04-15 12:40:32 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'BiocParallel' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for MsBackendRawFileReader on kjohnson3

To the developers/maintainers of the MsBackendRawFileReader package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendRawFileReader.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MsBackendRawFileReader
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendRawFileReader_1.14.0.tar.gz
StartedAt: 2025-04-21 20:31:25 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 20:33:34 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 129.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendRawFileReader.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendRawFileReader_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ 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 ‘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 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 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
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
ioBenchmark                  36.721  9.064  12.957
MsBackendRawFileReader        8.764  3.873  12.800
MsBackendRawFileReader-class  3.432  1.456   5.221
* 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


Installation output

MsBackendRawFileReader.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendRawFileReader
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘MsBackendRawFileReader’ ...
** this is package ‘MsBackendRawFileReader’ version ‘1.14.0’
** 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)

Tests output

MsBackendRawFileReader.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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
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:utils':

    findMatches

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

    I, expand.grid, unname

Loading required package: BiocParallel
> 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 21 ]

══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• isFALSE(file.exists(sample_mzXML_file)) is TRUE (1):
  'test_MsBackendMzR_MsBackendRawFileReader.R:1:1'
• isFALSE(require(MsBackendRawMgf)) is TRUE (1): 'test_top_n_mgf.R:1:1'

[ FAIL 0 | WARN 1 | SKIP 2 | PASS 21 ]
> 
> 
> 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 | peaks_variables                                                
⠙ |          2 | peaks_variables                                                
⠸ |          4 | peaks_variables                                                
✔ |          4 | peaks_variables [4.1s]

⠏ |          0 | spectra_subsetting                                             
⠋ |          1 | spectra_subsetting                                             
⠦ |         47 | spectra_subsetting                                             
⠼ |         85 | spectra_subsetting                                             
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⠧ |        2248 | spectra_subsetting                                            
⠴ |        2256 | spectra_subsetting                                            
⠸ |        2264 | spectra_subsetting                                            
⠙ |        2272 | spectra_subsetting                                            
⠏ |        2280 | spectra_subsetting                                            
⠧ |        2288 | spectra_subsetting                                            
⠴ |        2296 | spectra_subsetting                                            
⠇ |        2309 | spectra_subsetting                                            
⠹ |        2333 | spectra_subsetting                                            
✔ |        2342 | spectra_subsetting [12.6s]

⠏ |          0 | spectra_variables                                              
⠙ |         12 | spectra_variables                                              
⠸ |         14 | spectra_variables                                              
⠴ |         16 | spectra_variables                                              
⠦ |         27 | spectra_variables                                              
⠇ |         29 | spectra_variables                                              
⠋ |         31 | spectra_variables                                              
⠹ |         43 | spectra_variables                                              
✔ |      1  62 | spectra_variables [14.6s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 31.3 s

── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 2408 ]
> 
> proc.time()
   user  system elapsed 
 51.224  13.668  65.379 

Example timings

MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings

nameusersystemelapsed
MsBackendRawFileReader-class3.4321.4565.221
MsBackendRawFileReader 8.764 3.87312.800
hidden_aliases2.8111.2624.037
ioBenchmark36.721 9.06412.957