Johannes Rainer
| Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/MsBackendMsp |
| git_branch: RELEASE_3_21 |
| git_last_commit: 5d6dc9b |
| git_last_commit_date: 2025-04-15 12:46:17 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-18 11:42 -0400 (Mon, 18 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 1360/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MsBackendMsp 1.12.0 (landing page) Johannes Rainer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the MsBackendMsp package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsBackendMsp.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: MsBackendMsp |
| Version: 1.12.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MsBackendMsp.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MsBackendMsp_1.12.0.tar.gz |
| StartedAt: 2025-08-15 04:30:35 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 04:32:18 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 103.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MsBackendMsp.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MsBackendMsp.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MsBackendMsp_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MsBackendMsp.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MsBackendMsp/DESCRIPTION' ... OK
* this is package 'MsBackendMsp' version '1.12.0'
* 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 whether package 'MsBackendMsp' 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
* 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
MsBackendMsp.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MsBackendMsp ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'MsBackendMsp' ... ** this is package 'MsBackendMsp' version '1.12.0' ** using staged installation ** R ** inst ** 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 (MsBackendMsp)
MsBackendMsp.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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(MsBackendMsp)
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
>
> ## Run specific (backend) package tests
> test_check("MsBackendMsp")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 97 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 97 ]
>
> ## Run additional tests from Spectra:
> test_suite <- system.file("test_backends", "test_MsBackend",
+ package = "Spectra")
>
> fls <- system.file("extdata", "minimona.msp", package = "MsBackendMsp")
> be <- MsBackendMsp()
> be <- backendInitialize(
+ be, fls, mapping = spectraVariableMapping(MsBackendMsp(), "mona"))
>
> test_dir(test_suite, stop_on_failure = TRUE)
✔ | F W S OK | Context
⠏ | 0 | peaks_variables
✔ | 4 | peaks_variables
⠏ | 0 | spectra_subsetting
⠋ | 1 | spectra_subsetting
⠧ | 8 | spectra_subsetting
⠙ | 22 | spectra_subsetting
⠋ | 31 | spectra_subsetting
⠏ | 40 | spectra_subsetting
⠏ | 50 | spectra_subsetting
⠋ | 61 | spectra_subsetting
⠏ | 70 | spectra_subsetting
⠇ | 79 | spectra_subsetting
⠧ | 88 | spectra_subsetting
⠼ | 95 | spectra_subsetting
⠦ | 97 | spectra_subsetting
⠇ | 99 | spectra_subsetting
⠋ | 101 | spectra_subsetting
⠹ | 103 | spectra_subsetting
⠼ | 105 | spectra_subsetting
⠦ | 107 | spectra_subsetting
⠧ | 108 | spectra_subsetting
⠋ | 111 | spectra_subsetting
⠹ | 113 | spectra_subsetting
⠼ | 115 | spectra_subsetting
⠦ | 117 | spectra_subsetting
⠇ | 119 | spectra_subsetting
⠋ | 121 | spectra_subsetting
⠹ | 123 | spectra_subsetting
⠴ | 126 | spectra_subsetting
⠇ | 129 | spectra_subsetting
⠧ | 138 | spectra_subsetting
⠼ | 145 | spectra_subsetting
⠋ | 151 | spectra_subsetting
⠴ | 156 | spectra_subsetting
⠏ | 160 | spectra_subsetting
✔ | 166 | spectra_subsetting [4.5s]
⠏ | 0 | spectra_variables
⠦ | 7 | spectra_variables
⠦ | 17 | spectra_variables
⠧ | 28 | spectra_variables
⠦ | 37 | spectra_variables
⠼ | 45 | spectra_variables
⠇ | 59 | spectra_variables
⠏ | 70 | spectra_variables
⠧ | 78 | spectra_variables
✔ | 78 | spectra_variables [1.1s]
══ Results ═════════════════════════════════════════════════════════════════════
Duration: 5.7 s
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 248 ]
>
>
>
>
> proc.time()
user system elapsed
16.28 0.81 18.00
MsBackendMsp.Rcheck/MsBackendMsp-Ex.timings
| name | user | system | elapsed | |
| MsBackendMsp | 1.29 | 0.03 | 1.33 | |
| readMsp | 0.30 | 0.01 | 0.31 | |