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This page was generated on 2021-10-22 12:04:53 -0400 (Fri, 22 Oct 2021).

CHECK results for CluMSID on merida1

To the developers/maintainers of the CluMSID package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CluMSID.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 333/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CluMSID 1.9.0  (landing page)
Tobias Depke
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/CluMSID
git_branch: master
git_last_commit: 274ee44
git_last_commit_date: 2021-05-19 12:40:12 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CluMSID
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CluMSID_1.9.0.tar.gz
StartedAt: 2021-10-22 02:07:38 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 02:11:28 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 230.7 seconds
RetCode: 0
Status:   OK  
CheckDir: CluMSID.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CluMSID.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CluMSID_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/CluMSID.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CluMSID/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CluMSID’ version ‘1.9.0’
* 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 ‘CluMSID’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mergeMS2spectra 8.495  0.082   8.588
getSimilarities 5.221  0.045   5.273
* 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

CluMSID.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘CluMSID’ ...
** using staged installation
** R
** 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 (CluMSID)

Tests output

CluMSID.Rcheck/tests/testthat.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(CluMSID)
> 
> test_check("CluMSID")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 21.926   0.707  22.600 

Example timings

CluMSID.Rcheck/CluMSID-Ex.timings

nameusersystemelapsed
Featurelist0.0190.0010.075
HCplot0.5230.0080.578
HCtbl0.0170.0010.018
MDSplot0.9360.0190.956
OPTICSplot0.0380.0040.042
OPTICStbl0.0370.0030.039
accessors0.0920.0050.096
addAnnotations0.1380.0870.225
as.MS2spectrum0.2300.0170.246
cossim0.0410.0030.043
distanceMatrix1.0270.0851.114
extractMS2spectra1.9120.0711.986
extractPseudospectra1.9681.0262.314
findFragment0.0410.0000.041
findNL0.0340.0010.034
getSimilarities5.2210.0455.273
getSpectrum0.0340.0020.035
mergeMS2spectra8.4950.0828.588
networkplot0.2680.0030.272
specplot0.0120.0010.013
splitPolarities1.6880.0311.720
writeFeaturelist0.0250.0010.027