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CHECK report for MSstatsPTM on malbec1

This page was generated on 2021-05-06 12:28:20 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the MSstatsPTM package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1167/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsPTM 1.0.0  (landing page)
Tsung-Heng Tsai
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/MSstatsPTM
Branch: RELEASE_3_12
Last Commit: d8c642c
Last Changed Date: 2020-10-27 12:01:42 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: MSstatsPTM
Version: 1.0.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MSstatsPTM_1.0.0.tar.gz
StartedAt: 2021-05-06 03:47:24 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 03:48:07 -0400 (Thu, 06 May 2021)
EllapsedTime: 43.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsPTM.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:MSstatsPTM.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings MSstatsPTM_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/MSstatsPTM.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsPTM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MSstatsPTM’ 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 ‘MSstatsPTM’ 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
* 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

MSstatsPTM.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL MSstatsPTM
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘MSstatsPTM’ ...
** 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 (MSstatsPTM)

Tests output

MSstatsPTM.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(MSstatsPTM)
> 
> test_check("MSstatsPTM")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 40 ]
> 
> proc.time()
   user  system elapsed 
  1.628   0.072   1.701 

Example timings

MSstatsPTM.Rcheck/MSstatsPTM-Ex.timings

nameusersystemelapsed
PTMcompareMeans0.2400.0040.243
PTMestimate0.0960.0000.098
PTMlocate3.4320.0804.029
PTMnormalize0.1200.0000.118
PTMsimulateExperiment0.0960.0000.098
PTMsummarize0.1280.0040.134
adjustProteinLevel0.1880.0000.187
annotSite0.0000.0000.001
estimateAbundance0.2160.0000.218
extractMeanDiff0.1960.0000.196
fitLinearModel0.0120.0000.008
fixedGroup0.0040.0000.004
fixedGroupBatch0.0040.0000.005
locateMod000
simulatePeaks0.0280.0000.030
simulateSites0.0400.0000.038
simulateSummarization0.0240.0000.022
summarizeFeatures0.0320.0000.032
tidyEstimates0.0280.0040.033
tidyFasta0.1240.0040.700