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CHECK report for MSstatsTMT on merida2

This page was generated on 2019-04-09 13:37:42 -0400 (Tue, 09 Apr 2019).

Package 1043/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 1.1.2
Ting Huang
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MSstatsTMT
Branch: master
Last Commit: 5f454a7
Last Changed Date: 2019-02-25 14:20:12 -0400 (Mon, 25 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: MSstatsTMT
Version: 1.1.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsTMT_1.1.2.tar.gz
StartedAt: 2019-04-09 02:24:41 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:27:44 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 182.6 seconds
RetCode: 0
Status:  OK 
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MSstatsTMT_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MSstatsTMT.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MSstatsTMT/DESCRIPTION’ ... OK
* this is package ‘MSstatsTMT’ version ‘1.1.2’
* 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 or elapsed time > 5s
                       user system elapsed
dataProcessPlotsTMT  46.714  1.887  45.999
groupComparisonTMT   11.216  3.155   9.021
proteinSummarization  8.950  1.652   7.979
* 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:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MSstatsTMT
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘MSstatsTMT’ ...
** 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
* DONE (MSstatsTMT)

Tests output

MSstatsTMT.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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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     2   2     2 2    2
# of Technical Replicates      1   1     1 1    1

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══ testthat results  ═══════════════════════════════════════════════════════════
OK: 33 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.949   5.624  14.433 

Example timings

MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat2.0270.7970.900
PDtoMSstatsTMTFormat1.8690.6111.431
SpectroMinetoMSstatsTMTFormat0.5690.0580.634
annotation.mine0.0030.0000.003
annotation.mq0.0030.0010.004
annotation.pd0.0030.0000.003
dataProcessPlotsTMT46.714 1.88745.999
evidence0.1390.1070.036
groupComparisonTMT11.216 3.155 9.021
input.pd0.0110.0010.012
proteinGroups0.9160.7650.241
proteinSummarization8.9501.6527.979
quant.pd.msstats0.0210.0210.005
raw.mine0.0520.0530.015
raw.pd0.0820.0690.022
test.pairwise0.0140.0160.004