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CHECK report for MSstatsTMT on malbec2

This page was generated on 2020-10-17 11:55:13 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MSstatsTMT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1148/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 1.6.6
Ting Huang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MSstatsTMT
Branch: RELEASE_3_11
Last Commit: cbcd335
Last Changed Date: 2020-10-13 12:31:10 -0400 (Tue, 13 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MSstatsTMT
Version: 1.6.6
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSstatsTMT_1.6.6.tar.gz
StartedAt: 2020-10-17 03:29:57 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:32:54 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 176.5 seconds
RetCode: 0
Status:  OK 
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MSstatsTMT_1.6.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘1.6.6’
* 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 ‘MSstatsTMT’ 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
dataProcessPlotsTMT  39.642  0.180  39.287
groupComparisonTMT   19.048  0.092  18.468
proteinSummarization  6.520  0.047   5.894
* 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

MSstatsTMT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MSstatsTMT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MSstatsTMT’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (MSstatsTMT)

Tests output

MSstatsTMT.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(MSstatsTMT)
> 
> test_check("MSstatsTMT")
                       
  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     4-29
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-33
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-29
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-28
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     2-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     4-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     5-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     1-31
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     3-34
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     2-30
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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  Summary of Features :
                         count
# of Protein                10
# of Peptides/Protein     5-32
# of Transitions/Peptide   1-1
                      
  Summary of Samples :
                           0.125 0.5 0.667 1 Norm
# of MS runs                   2   2     2 2    2
# of Biological Replicates     1   1     1 1    1
# of Technical Replicates      2   2     2 2    2

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══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 26.911   0.333  26.024 

Example timings

MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.5160.0320.548
OpenMStoMSstatsTMTFormat0.5160.0120.527
PDtoMSstatsTMTFormat1.5030.0081.511
SpectroMinetoMSstatsTMTFormat0.5270.0120.540
annotation.mine0.0030.0000.003
annotation.mq0.0030.0000.003
annotation.pd0.0040.0000.003
dataProcessPlotsTMT39.642 0.18039.287
evidence0.0120.0040.016
groupComparisonTMT19.048 0.09218.468
input.pd0.0030.0040.007
proteinGroups0.0710.0120.083
proteinSummarization6.5200.0475.894
quant.pd.msstats0.0060.0000.005
raw.mine0.0130.0000.013
raw.om0.0070.0000.007
raw.pd0.0110.0000.011
test.pairwise0.0040.0000.004