Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-09 12:05 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1352/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsBackendRawFileReader 1.15.1  (landing page)
Christian Panse
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/MsBackendRawFileReader
git_branch: devel
git_last_commit: 1998d81
git_last_commit_date: 2025-06-12 03:00:23 -0400 (Thu, 12 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MsBackendRawFileReader on nebbiolo2

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: 1.15.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsBackendRawFileReader_1.15.1.tar.gz
StartedAt: 2025-08-09 00:31:55 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 00:36:41 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 286.2 seconds
RetCode: 0
Status:   OK  
CheckDir: MsBackendRawFileReader.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsBackendRawFileReader.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsBackendRawFileReader_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.15.1’
* 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 ‘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 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
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
ioBenchmark            30.863  6.117  11.487
MsBackendRawFileReader  6.411  2.142   9.077
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

MsBackendRawFileReader.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MsBackendRawFileReader
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MsBackendRawFileReader’ ...
** this is package ‘MsBackendRawFileReader’ version ‘1.15.1’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 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")
> 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

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⠋ |        2151 | spectra_subsetting                                            
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⠦ |        2157 | spectra_subsetting                                            
⠏ |        2160 | spectra_subsetting                                            
⠹ |        2163 | spectra_subsetting                                            
⠴ |        2166 | spectra_subsetting                                            
⠇ |        2169 | spectra_subsetting                                            
⠙ |        2172 | spectra_subsetting                                            
⠼ |        2175 | spectra_subsetting                                            
⠧ |        2178 | spectra_subsetting                                            
⠋ |        2181 | spectra_subsetting                                            
⠸ |        2184 | spectra_subsetting                                            
⠦ |        2187 | spectra_subsetting                                            
⠇ |        2189 | spectra_subsetting                                            
⠙ |        2192 | spectra_subsetting                                            
⠼ |        2195 | spectra_subsetting                                            
⠧ |        2198 | spectra_subsetting                                            
⠋ |        2201 | spectra_subsetting                                            
⠸ |        2204 | spectra_subsetting                                            
⠦ |        2207 | spectra_subsetting                                            
⠏ |        2210 | spectra_subsetting                                            
⠹ |        2213 | spectra_subsetting                                            
⠴ |        2216 | spectra_subsetting                                            
⠇ |        2219 | spectra_subsetting                                            
⠙ |        2222 | spectra_subsetting                                            
⠼ |        2225 | spectra_subsetting                                            
⠧ |        2228 | spectra_subsetting                                            
⠋ |        2231 | spectra_subsetting                                            
⠸ |        2234 | spectra_subsetting                                            
⠦ |        2237 | spectra_subsetting                                            
⠏ |        2240 | spectra_subsetting                                            
⠹ |        2243 | spectra_subsetting                                            
⠴ |        2246 | spectra_subsetting                                            
⠇ |        2249 | spectra_subsetting                                            
⠙ |        2252 | spectra_subsetting                                            
⠼ |        2255 | spectra_subsetting                                            
⠦ |        2257 | spectra_subsetting                                            
⠏ |        2260 | spectra_subsetting                                            
⠹ |        2263 | spectra_subsetting                                            
⠴ |        2266 | spectra_subsetting                                            
⠇ |        2269 | spectra_subsetting                                            
⠙ |        2272 | spectra_subsetting                                            
⠼ |        2275 | spectra_subsetting                                            
⠧ |        2278 | spectra_subsetting                                            
⠋ |        2281 | spectra_subsetting                                            
⠹ |        2283 | spectra_subsetting                                            
⠴ |        2286 | spectra_subsetting                                            
⠇ |        2289 | spectra_subsetting                                            
⠙ |        2292 | spectra_subsetting                                            
⠼ |        2295 | spectra_subsetting                                            
⠧ |        2298 | spectra_subsetting                                            
⠙ |        2302 | spectra_subsetting                                            
⠴ |        2306 | spectra_subsetting                                            
⠸ |        2314 | spectra_subsetting                                            
⠙ |        2322 | spectra_subsetting                                            
⠋ |        2331 | spectra_subsetting                                            
⠸ |        2334 | spectra_subsetting                                            
✔ |        2342 | spectra_subsetting [42.7s]

⠏ |          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                                              
✔ |      1  62 | spectra_variables [14.2s]

══ Results ═════════════════════════════════════════════════════════════════════
Duration: 60.8 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 
 82.390   7.974  92.929 

Example timings

MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings

nameusersystemelapsed
MsBackendRawFileReader-class3.0580.7704.037
MsBackendRawFileReader6.4112.1429.077
hidden_aliases2.1310.7233.032
ioBenchmark30.863 6.11711.487