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This page was generated on 2023-10-20 09:38:07 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1313/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsQuality 1.0.0  (landing page)
Thomas Naake
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/MsQuality
git_branch: RELEASE_3_17
git_last_commit: e4e396a
git_last_commit_date: 2023-04-25 11:41:52 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for MsQuality on kjohnson2


To the developers/maintainers of the MsQuality package:
- 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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2023-10-18 09:59:09 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 10:07:27 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 498.3 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_1.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MsQuality.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MsQuality/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MsQuality’ version ‘1.0.0’
* 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 R 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                 5.141  0.955   6.114
calculateMetricsFromMsExperiment 4.077  0.862   6.162
calculateMetricsFromSpectra      3.580  0.729   5.080
plotMetric                       3.004  0.677  10.518
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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, sort, 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")
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 193 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 193 ]
> 
> proc.time()
   user  system elapsed 
 50.314   6.961  73.288 

Example timings

MsQuality.Rcheck/MsQuality-Ex.timings

nameusersystemelapsed
MsQuality-package000
areaUnderTic2.5430.0284.013
areaUnderTicRtQuantiles0.2400.0090.383
calculateMetrics5.1410.9556.114
calculateMetricsFromMsExperiment4.0770.8626.162
calculateMetricsFromOneSampleSpectra2.4070.2744.200
calculateMetricsFromSpectra3.5800.7295.080
dot-rtOrderSpectra0.1890.0450.313
extentIdentifiedPrecursorIntensity0.1710.0160.249
meanCharge0.1610.0130.273
medianCharge0.1600.0120.268
medianPrecursorMz0.1610.0140.277
medianTicOfRtRange0.1610.0120.266
medianTicRtIqr0.1600.0130.267
msSignal10xChange0.1620.0140.270
mzAcquisitionRange0.1690.0160.291
numberSpectra0.1560.0120.259
plotMetric 3.004 0.67710.518
plotMetricTibble2.7880.6473.484
precursorIntensityMean0.1680.0190.289
precursorIntensityQuartiles0.1670.0160.287
precursorIntensityRange0.1670.0170.284
precursorIntensitySd0.1640.0130.273
qualityMetrics0.1660.0140.292
ratioCharge1over20.1670.0120.275
ratioCharge3over20.1640.0120.270
ratioCharge4over20.2050.0280.367
rtAcquisitionRange0.1640.0080.263
rtDuration0.1670.0100.270
rtIqr0.1690.0110.265
rtIqrRate0.1710.0110.266
rtOverMsQuarters0.1690.0110.270
rtOverTicQuantiles0.1650.0110.258
shinyMsQuality1.6230.4033.314
ticQuartileToQuartileLogRatio0.1780.0410.334