Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-09-23 12:03 -0400 (Tue, 23 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4816
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4605
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4549
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4560
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 1381/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsQuality 1.9.2  (landing page)
Thomas Naake
Snapshot Date: 2025-09-22 13:45 -0400 (Mon, 22 Sep 2025)
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: devel
git_last_commit: 4d444d5
git_last_commit_date: 2025-08-05 05:56:49 -0400 (Tue, 05 Aug 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MsQuality on nebbiolo2

To the developers/maintainers of the MsQuality package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MsQuality.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: MsQuality
Version: 1.9.2
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsQuality_1.9.2.tar.gz
StartedAt: 2025-09-23 02:02:08 -0400 (Tue, 23 Sep 2025)
EndedAt: 2025-09-23 02:10:31 -0400 (Tue, 23 Sep 2025)
EllapsedTime: 502.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MsQuality.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MsQuality_1.9.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MsQuality.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.9.2’
* 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 ‘MsQuality’ 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                   user system elapsed
calculateMetricsFromSpectra      12.625  2.367  10.931
calculateMetricsFromMsExperiment  6.145  1.639   4.576
calculateMetrics                  6.455  0.953   8.090
* 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

MsQuality.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘MsQuality’ ...
** this is package ‘MsQuality’ version ‘1.9.2’
** using staged installation
** R
** data
** 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 (MsQuality)

Tests output

MsQuality.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "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("MsQuality")
> library("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("MsExperiment")
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

The following object is masked from 'package:stats':

    smooth

> library("msdata")
> library("S4Vectors")
> 
> test_check("MsQuality")
trying URL 'https://api.github.com/repos/HUPO-PSI/psi-ms-CV/releases/latest'
Content type 'application/json; charset=utf-8' length 7775 bytes
==================================================
downloaded 7775 bytes

trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.201/psi-ms.obo'
Content type 'application/octet-stream' length 1030770 bytes (1006 KB)
==================================================
downloaded 1006 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 866 ]
> 
> proc.time()
   user  system elapsed 
105.404  22.287  84.585 

Example timings

MsQuality.Rcheck/MsQuality-Ex.timings

nameusersystemelapsed
MsQuality-package000
areaUnderTic0.2620.0210.353
areaUnderTicRtQuantiles0.2250.0000.278
calculateMetrics6.4550.9538.090
calculateMetricsFromMsExperiment6.1451.6394.576
calculateMetricsFromOneSampleSpectra3.9680.6583.155
calculateMetricsFromSpectra12.625 2.36710.931
chromatographyDuration0.1400.0090.149
dot-rtOrderSpectra0.1910.0140.205
extentIdentifiedPrecursorIntensity0.1350.0060.141
meanCharge0.1160.0090.126
medianCharge0.1150.0060.122
medianPrecursorMz0.1110.0050.115
medianTicOfRtRange0.1160.0060.122
medianTicRtIqr0.1230.0090.132
msSignal10xChange0.1360.0050.141
mzAcquisitionRange0.1350.0040.139
numberEmptyScans0.1430.0020.145
numberSpectra0.2140.0210.236
plotMetric2.7650.8782.732
plotMetricTibble2.2520.9051.772
precursorIntensityMean0.1210.0090.130
precursorIntensityQuartiles0.1210.0060.127
precursorIntensityRange0.1240.0090.133
precursorIntensitySd0.1160.0280.144
qualityMetrics0.1120.0170.129
ratioCharge1over20.1770.0340.212
ratioCharge3over20.1240.0040.129
ratioCharge4over20.1340.0130.147
rtAcquisitionRange0.1210.0030.125
rtIqr0.1300.0020.132
rtIqrRate0.1240.0010.126
rtOverMsQuarters0.1240.0300.154
shinyMsQuality1.3240.5601.680
ticQuantileRtFraction1.0240.2520.136
ticQuartileToQuartileLogRatio0.1260.0060.131
transformIntoMzQC2.0930.6801.497