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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1349/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsQuality 1.6.0  (landing page)
Thomas Naake
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: RELEASE_3_20
git_last_commit: 4638e53
git_last_commit_date: 2024-10-29 11:16:49 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MsQuality on kjohnson1

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: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsQuality_1.6.0.tar.gz
StartedAt: 2024-12-21 02:30:34 -0500 (Sat, 21 Dec 2024)
EndedAt: 2024-12-21 02:37:40 -0500 (Sat, 21 Dec 2024)
EllapsedTime: 426.1 seconds
RetCode: 0
Status:   OK  
CheckDir: MsQuality.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MsQuality_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MsQuality.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.6.0’
* 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 ‘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 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
calculateMetrics                     7.653  1.007   6.803
calculateMetricsFromMsExperiment     5.188  1.130   4.387
calculateMetricsFromOneSampleSpectra 4.704  0.648   3.539
* 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


Installation output

MsQuality.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MsQuality
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘MsQuality’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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("MsQuality")
> library("Spectra")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, 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 7326 bytes
==================================================
downloaded 7326 bytes

trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.186/psi-ms.obo'
Content type 'application/octet-stream' length 998930 bytes (975 KB)
==================================================
downloaded 975 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 866 ]
> 
> proc.time()
   user  system elapsed 
158.421  29.620 123.675 

Example timings

MsQuality.Rcheck/MsQuality-Ex.timings

nameusersystemelapsed
MsQuality-package000
areaUnderTic0.0860.0070.096
areaUnderTicRtQuantiles0.1140.0060.123
calculateMetrics7.6531.0076.803
calculateMetricsFromMsExperiment5.1881.1304.387
calculateMetricsFromOneSampleSpectra4.7040.6483.539
calculateMetricsFromSpectra3.2550.7053.851
chromatographyDuration0.1050.0320.137
dot-rtOrderSpectra0.1230.0210.145
extentIdentifiedPrecursorIntensity0.1150.0180.134
meanCharge0.1080.0120.120
medianCharge0.1020.0100.113
medianPrecursorMz0.1130.0130.128
medianTicOfRtRange0.1040.0160.120
medianTicRtIqr0.1110.0150.126
msSignal10xChange0.1170.0170.134
mzAcquisitionRange0.1030.0110.114
numberEmptyScans0.1080.0110.119
numberSpectra0.1270.0160.145
plotMetric3.6330.9313.609
plotMetricTibble3.2930.9172.511
precursorIntensityMean0.1150.0140.134
precursorIntensityQuartiles0.1190.0100.131
precursorIntensityRange0.1040.0080.113
precursorIntensitySd0.1080.0080.119
qualityMetrics0.1050.0070.115
ratioCharge1over20.0990.0070.110
ratioCharge3over20.1050.0080.126
ratioCharge4over20.1090.0090.126
rtAcquisitionRange0.1060.0090.114
rtIqr0.1070.0110.117
rtIqrRate0.1050.0160.120
rtOverMsQuarters0.1130.0160.129
shinyMsQuality1.8500.4532.177
ticQuartersRtFraction1.5150.2890.166
ticQuartileToQuartileLogRatio0.1100.0120.122
transformIntoMzQC0.3430.1680.404