Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-05-20 12:05:37 -0400 (Fri, 20 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4155
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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

CHECK results for MSstatsTMT on nebbiolo1


To the developers/maintainers of the MSstatsTMT package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MSstatsTMT.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1267/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MSstatsTMT 2.4.0  (landing page)
Ting Huang
Snapshot Date: 2022-05-19 13:55:15 -0400 (Thu, 19 May 2022)
git_url: https://git.bioconductor.org/packages/MSstatsTMT
git_branch: RELEASE_3_15
git_last_commit: 6d58793
git_last_commit_date: 2022-04-26 11:51:28 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: MSstatsTMT
Version: 2.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSstatsTMT_2.4.0.tar.gz
StartedAt: 2022-05-19 20:31:18 -0400 (Thu, 19 May 2022)
EndedAt: 2022-05-19 20:33:18 -0400 (Thu, 19 May 2022)
EllapsedTime: 120.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MSstatsTMT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:MSstatsTMT.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings MSstatsTMT_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/MSstatsTMT.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘2.4.0’
* 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 ‘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 ... NOTE
.checkRepeatedMeasures: no visible global function definition for ‘.’
.checkSingleSubject: no visible global function definition for ‘.’
.checkTechReplicate: no visible global function definition for ‘.’
.getGroupLabel: no visible binding for global variable ‘Condition’
.handleSingleContrastTMT: no visible global function definition for
  ‘.mygrad’
.plotProfileTMT: no visible global function definition for ‘.’
.plotProfileTMT: no visible binding for global variable ‘censored’
Undefined global functions or variables:
  . .mygrad Condition censored
* 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 LazyData ... 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 31.384  0.440  30.617
groupComparisonTMT   7.130  0.088   6.047
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/MSstatsTMT.Rcheck/00check.log’
for details.



Installation output

MSstatsTMT.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL MSstatsTMT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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")
INFO  [2022-05-19 20:33:08] ** Raw data from ProteomeDiscoverer imported successfully.
INFO  [2022-05-19 20:33:09] ** Raw data from ProteomeDiscoverer cleaned successfully.
INFO  [2022-05-19 20:33:09] ** Using provided annotation.
INFO  [2022-05-19 20:33:09] ** Raw data from MaxQuant imported successfully.
INFO  [2022-05-19 20:33:09] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-05-19 20:33:09] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-05-19 20:33:09] ** Rows with values of Potentialcontaminant equal to + are removed 
INFO  [2022-05-19 20:33:09] ** Rows with values of Reverse equal to + are removed 
INFO  [2022-05-19 20:33:09] ** + Contaminant, + Reverse, + Potential.contaminant proteins are removed.
INFO  [2022-05-19 20:33:09] ** Features with all missing measurements across channels within each run are removed.
INFO  [2022-05-19 20:33:09] ** Raw data from MaxQuant cleaned successfully.
INFO  [2022-05-19 20:33:09] ** Using provided annotation.
INFO  [2022-05-19 20:33:09] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2022-05-19 20:33:09] ** The following options are used:
  - Features will be defined by the columns: PeptideSequence, PrecursorCharge
  - Shared peptides will be removed.
  - Proteins with single feature will not be removed.
  - Features with less than 3 measurements within each run will be removed.
INFO  [2022-05-19 20:33:09] ** Features with all missing measurements across channels within each run are removed.
INFO  [2022-05-19 20:33:09] ** Shared peptides are removed.
INFO  [2022-05-19 20:33:09] ** Features with one or two measurements across channels within each run are removed.
INFO  [2022-05-19 20:33:09] ** PSMs have been aggregated to peptide ions.
INFO  [2022-05-19 20:33:09] ** Raw data from SpectroMine imported successfully.
INFO  [2022-05-19 20:33:09] ** Raw data from SpectroMine cleaned successfully.
INFO  [2022-05-19 20:33:09] ** Using provided annotation.
INFO  [2022-05-19 20:33:09] ** Run and Channel labels were standardized to remove symbols such as '.' or '%'.
INFO  [2022-05-19 20:33:09] Design: 5 mixtures.
INFO  [2022-05-19 20:33:09] Design: 3 technical replicated MS runs per mixture.
INFO  [2022-05-19 20:33:09] Design: 1 subject per condition (No biological variation).
INFO  [2022-05-19 20:33:09] Model fitting for 10 proteins.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:10] Testing for 10 proteins:

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:10] Design: 5 mixtures.
INFO  [2022-05-19 20:33:10] Design: 3 technical replicated MS runs per mixture.
INFO  [2022-05-19 20:33:10] Design: 1 subject per condition (No biological variation).
INFO  [2022-05-19 20:33:10] Model fitting for 10 proteins.

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:11] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:11] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:11] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_02raw ( 2  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:12] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_01raw ( 3  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:12] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_02raw ( 4  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:12] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture2_03raw ( 5  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:12] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_01raw ( 6  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:12] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_02raw ( 7  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:13] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_01raw ( 8  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:13] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_02raw ( 9  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:13] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_01raw ( 10  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_02raw ( 11  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture4_03raw ( 12  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture5_03raw ( 13  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:14] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_03raw ( 14  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:15] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture3_03raw ( 15  of  15 )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |==============                                                        |  20%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |========================================================              |  80%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |======================================================================| 100%
INFO  [2022-05-19 20:33:15] ** Protein-level summarization done by MSstats.
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] ** MSstatsTMT - proteinSummarization function
INFO  [2022-05-19 20:33:15] Summarizing for Run : 161117_SILAC_HeLa_UPS1_TMT10_Mixture1_01raw ( 1  of  15 )
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 27 ]
> 
> proc.time()
   user  system elapsed 
 11.097   0.405  10.169 

Example timings

MSstatsTMT.Rcheck/MSstatsTMT-Ex.timings

nameusersystemelapsed
MaxQtoMSstatsTMTFormat0.7360.0840.701
OpenMStoMSstatsTMTFormat0.1720.0040.166
PDtoMSstatsTMTFormat1.7350.0561.624
SpectroMinetoMSstatsTMTFormat0.2610.0080.263
annotation.mine0.0020.0000.002
annotation.mq0.0000.0020.001
annotation.pd0.0010.0010.002
dataProcessPlotsTMT31.384 0.44030.617
evidence0.0050.0080.013
groupComparisonTMT7.1300.0886.047
input.pd0.0270.0080.034
proteinGroups0.0380.0440.082
proteinSummarization4.8150.0593.783
quant.pd.msstats0.0280.0050.029
raw.mine0.0020.0030.006
raw.om0.0030.0000.003
raw.pd0.0030.0030.007
test.pairwise0.0020.0000.002