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This page was generated on 2023-10-16 11:37:17 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1313/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MsQuality 1.0.0  (landing page)
Thomas Naake
Snapshot Date: 2023-10-15 14:00:13 -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)
nebbiolo1Linux (Ubuntu 22.04.2 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
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for MsQuality on merida1


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: 1.0.0
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: 2023-10-16 04:21:48 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 04:33:32 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 703.7 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/MsQuality.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* 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
plotMetricTibble                     6.248  4.163   7.017
calculateMetricsFromMsExperiment     7.634  2.575   7.257
ticQuartileToQuartileLogRatio        5.575  4.092   0.425
calculateMetricsFromOneSampleSpectra 6.634  1.683   4.824
calculateMetricsFromSpectra          5.251  1.660   5.906
calculateMetrics                     4.778  1.414   7.098
plotMetric                           4.488  1.456  10.975
shinyMsQuality                       0.889  0.361   7.001
* 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

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/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: x86_64-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 
 79.261  16.809  92.722 

Example timings

MsQuality.Rcheck/MsQuality-Ex.timings

nameusersystemelapsed
MsQuality-package0.0000.0010.001
areaUnderTic3.2880.0534.678
areaUnderTicRtQuantiles0.3840.0130.506
calculateMetrics4.7781.4147.098
calculateMetricsFromMsExperiment7.6342.5757.257
calculateMetricsFromOneSampleSpectra6.6341.6834.824
calculateMetricsFromSpectra5.2511.6605.906
dot-rtOrderSpectra1.7700.4980.389
extentIdentifiedPrecursorIntensity0.2100.0270.300
meanCharge0.2170.0240.311
medianCharge0.2180.0250.324
medianPrecursorMz0.2080.0230.297
medianTicOfRtRange0.2090.0240.302
medianTicRtIqr0.2180.0230.317
msSignal10xChange0.2190.0240.326
mzAcquisitionRange0.2250.0250.317
numberSpectra0.2010.0240.302
plotMetric 4.488 1.45610.975
plotMetricTibble6.2484.1637.017
precursorIntensityMean0.2200.0350.297
precursorIntensityQuartiles0.2120.0290.304
precursorIntensityRange0.2140.0260.308
precursorIntensitySd0.2190.0270.304
qualityMetrics0.2210.0260.311
ratioCharge1over20.2350.0260.326
ratioCharge3over20.2200.0230.308
ratioCharge4over20.2210.0230.312
rtAcquisitionRange0.2110.0210.288
rtDuration0.2130.0210.309
rtIqr0.2160.0220.312
rtIqrRate0.2130.0210.303
rtOverMsQuarters0.2070.0220.314
rtOverTicQuantiles0.2110.0210.321
shinyMsQuality0.8890.3617.001
ticQuartileToQuartileLogRatio5.5754.0920.425