| Back to Multiple platform build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-05-26 11:36 -0400 (Tue, 26 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4938 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There" | 4640 |
| 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 1387/2379 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMetaboLights 1.7.1 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | | |||||||||
| See other builds for MsBackendMetaboLights in R Universe. | ||||||||||||||
|
To the developers/maintainers of the MsBackendMetaboLights package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMetaboLights.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: MsBackendMetaboLights |
| Version: 1.7.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.7.1.tar.gz |
| StartedAt: 2026-05-25 20:38:26 -0400 (Mon, 25 May 2026) |
| EndedAt: 2026-05-25 20:44:08 -0400 (Mon, 25 May 2026) |
| EllapsedTime: 342.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendMetaboLights.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsBackendMetaboLights.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsBackendMetaboLights_1.7.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.24-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R version 4.6.0 Patched (2026-05-01 r89994)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-05-26 00:38:26 UTC
* using option ‘--no-vignettes’
* checking for file ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.7.1’
* 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 ‘MsBackendMetaboLights’ 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
MsBackendMetaboLights 2.760 0.599 9.795
MetaboLights-utils 0.153 0.025 12.373
* 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
MsBackendMetaboLights.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsBackendMetaboLights ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘MsBackendMetaboLights’ ... ** this is package ‘MsBackendMetaboLights’ version ‘1.7.1’ ** using staged installation ** R ** 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 (MsBackendMetaboLights)
MsBackendMetaboLights.Rcheck/tests/testthat.Rout
R version 4.6.0 Patched (2026-05-01 r89994) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23
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.
> #' MetaboLights ID: MTBLS8735
> #' ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS8735
>
> library(testthat)
> library(MsBackendMetaboLights)
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 object is masked from 'package:utils':
data
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
>
> test_check("MsBackendMetaboLights")
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 97 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 97 ]
>
> ## Run tests with the unit test suite defined in the Spectra package to ensure
> ## compliance with the definitions of the MsBackend interface/class.
> be <- backendInitialize(MsBackendMetaboLights(), mtblsId = "MTBLS39",
+ filePattern = "63A.cdf")
Used data files from the assay's column "Raw Spectral Data File" since none were available in column "Derived Spectral Data File".
>
> library(Spectra)
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
> 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
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠧ | 38 | spectra_subsetting
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⠹ | 673 | spectra_subsetting
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⠹ | 1643 | spectra_subsetting
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⠏ | 1970 | spectra_subsetting
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⠹ | 2113 | spectra_subsetting
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⠇ | 2219 | spectra_subsetting
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⠹ | 2293 | spectra_subsetting
⠋ | 2331 | spectra_subsetting
⠧ | 2368 | spectra_subsetting
⠦ | 2407 | spectra_subsetting
⠋ | 2441 | spectra_subsetting
⠦ | 2477 | spectra_subsetting
⠙ | 2512 | spectra_subsetting
⠧ | 2548 | spectra_subsetting
⠸ | 2584 | spectra_subsetting
⠋ | 2621 | spectra_subsetting
⠇ | 2659 | spectra_subsetting
⠼ | 2695 | spectra_subsetting
⠙ | 2732 | spectra_subsetting
⠦ | 2767 | spectra_subsetting
⠏ | 2800 | spectra_subsetting
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⠼ | 2905 | spectra_subsetting
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⠸ | 3004 | spectra_subsetting
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⠹ | 3103 | spectra_subsetting
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⠋ | 3321 | spectra_subsetting
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⠏ | 3460 | spectra_subsetting
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⠴ | 3676 | spectra_subsetting
⠧ | 3708 | spectra_subsetting
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⠋ | 3781 | spectra_subsetting
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⠸ | 3854 | spectra_subsetting
⠴ | 3886 | spectra_subsetting
⠇ | 3919 | spectra_subsetting
⠼ | 3955 | spectra_subsetting
⠋ | 3991 | spectra_subsetting
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⠏ | 4060 | spectra_subsetting
⠹ | 4093 | spectra_subsetting
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⠹ | 6673 | spectra_subsetting
⠇ | 6679 | spectra_subsetting
⠸ | 6694 | spectra_subsetting
✔ | 6702 | spectra_subsetting [148.5s]
⠏ | 0 | spectra_variables
⠙ | 12 | spectra_variables
⠸ | 14 | spectra_variables
⠴ | 16 | spectra_variables
⠦ | 27 | spectra_variables
⠇ | 29 | spectra_variables
⠋ | 31 | spectra_variables
⠹ | 43 | spectra_variables
⠸ | 54 | spectra_variables
✔ | 1 62 | spectra_variables [1.8s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 150.6 s
── Skipped tests (1) ───────────────────────────────────────────────────────────
• empty test (1): 'test_spectra_variables.R:262:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 6768 ]
>
> proc.time()
user system elapsed
152.477 8.456 283.937
MsBackendMetaboLights.Rcheck/MsBackendMetaboLights-Ex.timings
| name | user | system | elapsed | |
| MetaboLights-utils | 0.153 | 0.025 | 12.373 | |
| MsBackendMetaboLights | 2.760 | 0.599 | 9.795 | |