| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:06 -0500 (Thu, 20 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 1375/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMetaboLights 1.4.2 (landing page) Johannes Rainer
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.4.2 |
| 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_1.4.2.tar.gz |
| StartedAt: 2025-11-18 09:39:45 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 09:49:09 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 564.8 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_1.4.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MsBackendMetaboLights.Rcheck’
* using R version 4.5.2 Patched (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 ‘MsBackendMetaboLights/DESCRIPTION’ ... OK
* this is package ‘MsBackendMetaboLights’ version ‘1.4.2’
* 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 4.548 0.727 35.457
MetaboLights-utils 0.140 0.014 8.499
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘MsBackendMetaboLights’ ... ** this is package ‘MsBackendMetaboLights’ version ‘1.4.2’ ** 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 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"
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.
> #' 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 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 0 | SKIP 0 | PASS 78 ]
>
> ## 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
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⠦ | 6247 | spectra_subsetting
⠇ | 6249 | spectra_subsetting
⠋ | 6251 | spectra_subsetting
⠹ | 6253 | spectra_subsetting
⠼ | 6255 | spectra_subsetting
⠦ | 6257 | spectra_subsetting
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⠋ | 6261 | spectra_subsetting
⠙ | 6262 | spectra_subsetting
⠸ | 6264 | spectra_subsetting
⠴ | 6266 | spectra_subsetting
⠦ | 6267 | spectra_subsetting
⠇ | 6269 | spectra_subsetting
⠋ | 6271 | spectra_subsetting
⠹ | 6273 | spectra_subsetting
⠼ | 6275 | spectra_subsetting
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⠋ | 6281 | spectra_subsetting
⠙ | 6282 | spectra_subsetting
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⠦ | 6287 | spectra_subsetting
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⠋ | 6291 | spectra_subsetting
⠙ | 6292 | spectra_subsetting
⠸ | 6294 | spectra_subsetting
⠴ | 6296 | spectra_subsetting
⠧ | 6298 | spectra_subsetting
⠏ | 6300 | spectra_subsetting
⠋ | 6301 | spectra_subsetting
⠹ | 6303 | spectra_subsetting
⠸ | 6304 | spectra_subsetting
⠼ | 6305 | spectra_subsetting
⠴ | 6306 | spectra_subsetting
⠦ | 6307 | spectra_subsetting
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⠏ | 6310 | spectra_subsetting
⠋ | 6311 | spectra_subsetting
⠙ | 6312 | spectra_subsetting
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⠼ | 6315 | spectra_subsetting
⠴ | 6316 | spectra_subsetting
⠦ | 6317 | spectra_subsetting
⠇ | 6319 | spectra_subsetting
⠏ | 6320 | spectra_subsetting
⠋ | 6321 | spectra_subsetting
⠙ | 6322 | spectra_subsetting
⠹ | 6323 | spectra_subsetting
⠸ | 6324 | spectra_subsetting
⠼ | 6325 | spectra_subsetting
⠴ | 6326 | spectra_subsetting
⠦ | 6327 | spectra_subsetting
⠧ | 6328 | spectra_subsetting
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⠏ | 6330 | spectra_subsetting
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⠸ | 6334 | spectra_subsetting
⠼ | 6335 | spectra_subsetting
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⠦ | 6337 | spectra_subsetting
⠧ | 6338 | spectra_subsetting
⠏ | 6340 | spectra_subsetting
⠋ | 6341 | spectra_subsetting
⠙ | 6342 | spectra_subsetting
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⠏ | 6350 | spectra_subsetting
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⠏ | 6370 | spectra_subsetting
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⠋ | 6391 | spectra_subsetting
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⠇ | 6399 | spectra_subsetting
⠋ | 6401 | spectra_subsetting
⠹ | 6403 | spectra_subsetting
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⠏ | 6410 | spectra_subsetting
⠋ | 6411 | spectra_subsetting
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⠏ | 6450 | spectra_subsetting
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⠏ | 6460 | spectra_subsetting
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⠏ | 6510 | spectra_subsetting
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⠴ | 6626 | spectra_subsetting
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⠏ | 6630 | spectra_subsetting
⠋ | 6631 | spectra_subsetting
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⠸ | 6634 | spectra_subsetting
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⠴ | 6636 | spectra_subsetting
⠦ | 6637 | spectra_subsetting
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⠴ | 6646 | spectra_subsetting
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⠹ | 6673 | spectra_subsetting
⠇ | 6679 | spectra_subsetting
⠇ | 6689 | spectra_subsetting
⠸ | 6694 | spectra_subsetting
✔ | 6702 | spectra_subsetting [194.2s]
⠏ | 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 [2.1s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 196.8 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
169.905 11.182 479.839
MsBackendMetaboLights.Rcheck/MsBackendMetaboLights-Ex.timings
| name | user | system | elapsed | |
| MetaboLights-utils | 0.140 | 0.014 | 8.499 | |
| MsBackendMetaboLights | 4.548 | 0.727 | 35.457 | |