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This page was generated on 2024-05-04 11:36:52 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1359/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsQuality 1.4.0  (landing page)
Thomas Naake
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: RELEASE_3_19
git_last_commit: 3bf7832
git_last_commit_date: 2024-04-30 11:46:25 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for MsQuality on nebbiolo1


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: 1.4.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MsQuality_1.4.0.tar.gz
StartedAt: 2024-05-04 01:25:10 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 01:31:28 -0400 (Sat, 04 May 2024)
EllapsedTime: 378.6 seconds
RetCode: 0
Status:   OK  
CheckDir: MsQuality.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:MsQuality.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings MsQuality_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/MsQuality.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.4.0’
* 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 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
calculateMetrics 6.793  1.065   6.434
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL MsQuality
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 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

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, 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
Loading required package: ProtGenerics

Attaching package: 'ProtGenerics'

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

    smooth

> library("MsExperiment")
> 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 7475 bytes
==================================================
downloaded 7475 bytes

trying URL 'https://github.com/HUPO-PSI/psi-ms-CV/releases/download/v4.1.153/psi-ms.obo'
Content type 'application/octet-stream' length 984819 bytes (961 KB)
==================================================
downloaded 961 KB

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 866 ]
> 
> proc.time()
   user  system elapsed 
108.334  22.575  86.068 

Example timings

MsQuality.Rcheck/MsQuality-Ex.timings

nameusersystemelapsed
MsQuality-package000
areaUnderTic0.1750.0130.187
areaUnderTicRtQuantiles0.1760.0040.179
calculateMetrics6.7931.0656.434
calculateMetricsFromMsExperiment3.3500.9362.918
calculateMetricsFromOneSampleSpectra3.8800.6792.193
calculateMetricsFromSpectra2.9380.8492.484
chromatographyDuration1.0390.2070.148
dot-rtOrderSpectra0.1510.0280.179
extentIdentifiedPrecursorIntensity0.1410.0040.145
meanCharge0.1100.0120.122
medianCharge0.1080.0280.136
medianPrecursorMz0.1030.0040.107
medianTicOfRtRange0.1220.0080.130
medianTicRtIqr0.1290.0040.133
msSignal10xChange0.1320.0080.140
mzAcquisitionRange0.1180.0160.134
numberEmptyScans0.1070.0560.163
numberSpectra0.1180.0040.122
plotMetric2.7310.8902.490
plotMetricTibble2.2931.0361.807
precursorIntensityMean0.0880.0200.108
precursorIntensityQuartiles0.1130.0140.126
precursorIntensityRange0.1060.0120.118
precursorIntensitySd0.0970.0000.097
qualityMetrics0.0950.0350.131
ratioCharge1over20.1150.0040.119
ratioCharge3over20.1010.0120.113
ratioCharge4over20.1070.0120.119
rtAcquisitionRange0.0810.0200.101
rtIqr0.0960.0040.099
rtIqrRate0.1010.0120.113
rtOverMsQuarters0.0930.0200.113
shinyMsQuality0.3780.2601.712
ticQuartersRtFraction2.0830.6240.119
ticQuartileToQuartileLogRatio0.1060.0080.113
transformIntoMzQC0.3030.2420.367