| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-26 11:35 -0500 (Fri, 26 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4774 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4594 |
| 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 1365/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendRawFileReader 1.17.0 (landing page) Christian Panse
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: MsBackendRawFileReader |
| Version: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2025-12-25 21:07:02 -0500 (Thu, 25 Dec 2025) |
| EndedAt: 2025-12-25 21:10:24 -0500 (Thu, 25 Dec 2025) |
| EllapsedTime: 201.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendRawFileReader.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/MsBackendRawFileReader.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsBackendRawFileReader/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsBackendRawFileReader’ version ‘1.17.0’
* 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 36.918 9.659 16.732
MsBackendRawFileReader 16.520 5.602 24.739
MsBackendRawFileReader-class 5.665 1.903 8.377
hidden_aliases 5.376 1.846 7.781
* 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
MsBackendRawFileReader.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendRawFileReader ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘MsBackendRawFileReader’ ... ** this is package ‘MsBackendRawFileReader’ version ‘1.17.0’ ** 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)
MsBackendRawFileReader.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
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 [7.6s]
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠦ | 37 | spectra_subsetting
⠇ | 79 | spectra_subsetting
⠋ | 121 | spectra_subsetting
⠏ | 160 | spectra_subsetting
⠴ | 196 | spectra_subsetting
⠇ | 229 | spectra_subsetting
⠴ | 266 | spectra_subsetting
⠋ | 301 | spectra_subsetting
⠦ | 337 | spectra_subsetting
⠹ | 373 | spectra_subsetting
⠇ | 409 | spectra_subsetting
⠧ | 448 | spectra_subsetting
⠏ | 480 | spectra_subsetting
⠧ | 508 | spectra_subsetting
⠦ | 547 | spectra_subsetting
⠇ | 589 | spectra_subsetting
⠼ | 625 | spectra_subsetting
⠋ | 661 | spectra_subsetting
⠦ | 697 | spectra_subsetting
⠸ | 734 | spectra_subsetting
⠹ | 773 | spectra_subsetting
⠧ | 808 | spectra_subsetting
⠹ | 843 | spectra_subsetting
⠏ | 880 | spectra_subsetting
⠹ | 913 | spectra_subsetting
⠙ | 952 | spectra_subsetting
⠼ | 985 | spectra_subsetting
⠧ | 1018 | spectra_subsetting
⠸ | 1054 | spectra_subsetting
⠦ | 1087 | spectra_subsetting
⠋ | 1121 | spectra_subsetting
⠴ | 1156 | spectra_subsetting
⠙ | 1192 | spectra_subsetting
⠼ | 1225 | spectra_subsetting
⠙ | 1262 | spectra_subsetting
⠏ | 1300 | spectra_subsetting
⠴ | 1336 | spectra_subsetting
⠸ | 1374 | spectra_subsetting
⠴ | 1406 | spectra_subsetting
⠸ | 1444 | spectra_subsetting
⠙ | 1482 | spectra_subsetting
⠹ | 1513 | spectra_subsetting
⠇ | 1549 | spectra_subsetting
⠧ | 1588 | spectra_subsetting
⠦ | 1627 | spectra_subsetting
⠴ | 1666 | spectra_subsetting
⠙ | 1702 | spectra_subsetting
⠧ | 1728 | spectra_subsetting
⠸ | 1734 | spectra_subsetting
⠏ | 1740 | spectra_subsetting
⠦ | 1747 | spectra_subsetting
⠹ | 1753 | spectra_subsetting
⠇ | 1759 | spectra_subsetting
⠼ | 1765 | spectra_subsetting
⠋ | 1771 | spectra_subsetting
⠦ | 1777 | spectra_subsetting
⠹ | 1783 | spectra_subsetting
⠇ | 1789 | spectra_subsetting
⠼ | 1795 | spectra_subsetting
⠋ | 1801 | spectra_subsetting
⠦ | 1807 | spectra_subsetting
⠹ | 1813 | spectra_subsetting
⠇ | 1819 | spectra_subsetting
⠼ | 1825 | spectra_subsetting
⠋ | 1831 | spectra_subsetting
⠦ | 1837 | spectra_subsetting
⠹ | 1843 | spectra_subsetting
⠧ | 1848 | spectra_subsetting
⠋ | 1851 | spectra_subsetting
⠦ | 1857 | spectra_subsetting
⠹ | 1863 | spectra_subsetting
⠇ | 1869 | spectra_subsetting
⠴ | 1876 | spectra_subsetting
⠹ | 1883 | spectra_subsetting
⠇ | 1889 | spectra_subsetting
⠴ | 1896 | spectra_subsetting
⠹ | 1903 | spectra_subsetting
⠏ | 1910 | spectra_subsetting
⠦ | 1917 | spectra_subsetting
⠸ | 1924 | spectra_subsetting
⠋ | 1931 | spectra_subsetting
⠧ | 1938 | spectra_subsetting
⠴ | 1946 | spectra_subsetting
⠙ | 1952 | spectra_subsetting
⠇ | 1959 | spectra_subsetting
⠼ | 1965 | spectra_subsetting
⠙ | 1972 | spectra_subsetting
⠇ | 1979 | spectra_subsetting
⠴ | 1986 | spectra_subsetting
⠹ | 1993 | spectra_subsetting
⠏ | 2000 | spectra_subsetting
⠴ | 2006 | spectra_subsetting
⠹ | 2013 | spectra_subsetting
⠏ | 2020 | spectra_subsetting
⠦ | 2027 | spectra_subsetting
⠸ | 2034 | spectra_subsetting
⠋ | 2041 | spectra_subsetting
⠦ | 2047 | spectra_subsetting
⠸ | 2054 | spectra_subsetting
⠋ | 2061 | spectra_subsetting
⠧ | 2068 | spectra_subsetting
⠸ | 2074 | spectra_subsetting
⠋ | 2081 | spectra_subsetting
⠇ | 2089 | spectra_subsetting
⠴ | 2096 | spectra_subsetting
⠹ | 2103 | spectra_subsetting
⠏ | 2110 | spectra_subsetting
⠦ | 2117 | spectra_subsetting
⠸ | 2124 | spectra_subsetting
⠋ | 2131 | spectra_subsetting
⠧ | 2138 | spectra_subsetting
⠼ | 2145 | spectra_subsetting
⠙ | 2152 | spectra_subsetting
⠇ | 2159 | spectra_subsetting
⠦ | 2167 | spectra_subsetting
⠸ | 2174 | spectra_subsetting
⠋ | 2181 | spectra_subsetting
⠧ | 2188 | spectra_subsetting
⠼ | 2195 | spectra_subsetting
⠙ | 2202 | spectra_subsetting
⠇ | 2209 | spectra_subsetting
⠴ | 2216 | spectra_subsetting
⠹ | 2223 | spectra_subsetting
⠏ | 2230 | spectra_subsetting
⠦ | 2237 | spectra_subsetting
⠸ | 2244 | spectra_subsetting
⠋ | 2251 | spectra_subsetting
⠦ | 2257 | spectra_subsetting
⠸ | 2264 | spectra_subsetting
⠋ | 2271 | spectra_subsetting
⠧ | 2278 | spectra_subsetting
⠼ | 2285 | spectra_subsetting
⠋ | 2291 | spectra_subsetting
⠧ | 2298 | spectra_subsetting
⠹ | 2313 | spectra_subsetting
⠸ | 2334 | spectra_subsetting
✔ | 2342 | spectra_subsetting [14.9s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠹ | 23 | spectra_variables
⠦ | 27 | spectra_variables
⠇ | 29 | spectra_variables
⠋ | 31 | spectra_variables
⠹ | 43 | spectra_variables
⠋ | 1 60 | spectra_variables
✔ | 1 62 | spectra_variables [25.8s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 48.3 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
81.974 20.289 110.022
MsBackendRawFileReader.Rcheck/MsBackendRawFileReader-Ex.timings
| name | user | system | elapsed | |
| MsBackendRawFileReader-class | 5.665 | 1.903 | 8.377 | |
| MsBackendRawFileReader | 16.520 | 5.602 | 24.739 | |
| hidden_aliases | 5.376 | 1.846 | 7.781 | |
| ioBenchmark | 36.918 | 9.659 | 16.732 | |